2014 Top Genetic Genealogy Happenings – A Baker’s Dozen +1

It’s that time again, to look over the year that has just passed and take stock of what has happened in the genetic genealogy world.  I wrote a review in both 2012 and 2013 as well.  Looking back, these momentous happenings seem quite “old hat” now.  For example, both www.GedMatch.com and www.DNAGedcom.com, once new, have become indispensable tools that we take for granted.  Please keep in mind that both of these tools (as well as others in the Tools section, below) depend on contributions, although GedMatch now has a tier 1 subscription offering for $10 per month as well.

So what was the big news in 2014?

Beyond the Tipping Point

Genetic genealogy has gone over the tipping point.  Genetic genealogy is now, unquestionably, mainstream and lots of people are taking part.  From the best I can figure, there are now approaching or have surpassed three million tests or test records, although certainly some of those are duplicates.

  • 500,000+ at 23andMe
  • 700,000+ at Ancestry
  • 700,000+ at Genographic

The organizations above represent “one-test” companies.  Family Tree DNA provides various kinds of genetic genealogy tests to the community and they have over 380,000 individuals with more than 700,000 test records.

In addition to the above mentioned mainstream firms, there are other companies that provide niche testing, often in addition to Family Tree DNA Y results.

In addition, there is what I would refer to as a secondary market for testing as well which certainly attracts people who are not necessarily genetic genealogists but who happen across their corporate information and decide the test looks interesting.  There is no way of knowing how many of those tests exist.

Additionally, there is still the Sorenson data base with Y and mtDNA tests which reportedly exceeded their 100,000 goal.

Spencer Wells spoke about the “viral spread threshold” in his talk in Houston at the International Genetic Genealogy Conference in October and terms 2013 as the year of infection.  I would certainly agree.

spencer near term

Autosomal Now the New Normal

Another change in the landscape is that now, autosomal DNA has become the “normal” test.  The big attraction to autosomal testing is that anyone can play and you get lots of matches.  Earlier in the year, one of my cousins was very disappointed in her brother’s Y DNA test because he only had a few matches, and couldn’t understand why anyone would test the Y instead of autosomal where you get lots and lots of matches.  Of course, she didn’t understand the difference in the tests or the goals of the tests – but I think as more and more people enter the playground – percentagewise – fewer and fewer do understand the differences.

Case in point is that someone contacted me about DNA and genealogy.  I asked them which tests they had taken and where and their answer was “the regular one.”  With a little more probing, I discovered that they took Ancestry’s autosomal test and had no clue there were any other types of tests available, what they could tell him about his ancestors or genetic history or that there were other vendors and pools to swim in as well.

A few years ago, we not only had to explain about DNA tests, but why the Y and mtDNA is important.  Today, we’ve come full circle in a sense – because now we don’t have to explain about DNA testing for genealogy in general but we still have to explain about those “unknown” tests, the Y and mtDNA.  One person recently asked me, “oh, are those new?”

Ancient DNA

This year has seen many ancient DNA specimens analyzed and sequenced at the full genomic level.

The year began with a paper titled, “When Populations Collide” which revealed that contemporary Europeans carry between 1-4% of Neanderthal DNA most often associated with hair and skin color, or keratin.  Africans, on the other hand, carry none or very little Neanderthal DNA.

https://dna-explained.com/2014/01/30/neanderthal-genome-further-defined-in-contemporary-eurasians/

A month later, a monumental paper was published that detailed the results of sequencing a 12,500 Clovis child, subsequently named Anzick or referred to as the Anzick Clovis child, in Montana.  That child is closely related to Native American people of today.

https://dna-explained.com/2014/02/13/clovis-people-are-native-americans-and-from-asia-not-europe/

In June, another paper emerged where the authors had analyzed 8000 year old bones from the Fertile Crescent that shed light on the Neolithic area before the expansion from the Fertile Crescent into Europe.  These would be the farmers that assimilated with or replaced the hunter-gatherers already living in Europe.

https://dna-explained.com/2014/06/09/dna-analysis-of-8000-year-old-bones-allows-peek-into-the-neolithic/

Svante Paabo is the scientist who first sequenced the Neanderthal genome.  Here is a neanderthal mangreat interview and speech.  This man is so interesting.  If you have not read his book, “Neanderthal Man, In Search of Lost Genomes,” I strongly recommend it.

https://dna-explained.com/2014/07/22/finding-your-inner-neanderthal-with-evolutionary-geneticist-svante-paabo/

In the fall, yet another paper was released that contained extremely interesting information about the peopling and migration of humans across Europe and Asia.  This was just before Michael Hammer’s presentation at the Family Tree DNA conference, so I covered the paper along with Michael’s information about European ancestral populations in one article.  The take away messages from this are two-fold.  First, there was a previously undefined “ghost population” called Ancient North Eurasian (ANE) that is found in the northern portion of Asia that contributed to both Asian populations, including those that would become the Native Americans and European populations as well.  Secondarily, the people we thought were in Europe early may not have been, based on the ancient DNA remains we have to date.  Of course, that may change when more ancient DNA is fully sequenced which seems to be happening at an ever-increasing rate.

https://dna-explained.com/2014/10/21/peopling-of-europe-2014-identifying-the-ghost-population/

Lazaridis tree

Ancient DNA Available for Citizen Scientists

If I were to give a Citizen Scientist of the Year award, this year’s award would go unquestionably to Felix Chandrakumar for his work with the ancient genome files and making them accessible to the genetic genealogy world.  Felix obtained the full genome files from the scientists involved in full genome analysis of ancient remains, reduced the files to the SNPs utilized by the autosomal testing companies in the genetic genealogy community, and has made them available at GedMatch.

https://dna-explained.com/2014/09/22/utilizing-ancient-dna-at-gedmatch/

If this topic is of interest to you, I encourage you to visit his blog and read his many posts over the past several months.

https://plus.google.com/+FelixChandrakumar/posts

The availability of these ancient results set off a sea of comparisons.  Many people with Native heritage matched Anzick’s file at some level, and many who are heavily Native American, particularly from Central and South America where there is less admixture match Anzick at what would statistically be considered within a genealogical timeframe.  Clearly, this isn’t possible, but it does speak to how endogamous populations affect DNA, even across thousands of years.

https://dna-explained.com/2014/09/23/analyzing-the-native-american-clovis-anzick-ancient-results/

Because Anzick is matching so heavily with the Mexican, Central and South American populations, it gives us the opportunity to extract mitochondrial DNA haplogroups from the matches that either are or may be Native, if they have not been recorded before.

https://dna-explained.com/2014/09/23/analyzing-the-native-american-clovis-anzick-ancient-results/

Needless to say, the matches of these ancient kits with contemporary people has left many people questioning how to interpret the results.  The answer is that we don’t really know yet, but there is a lot of study as well as speculation occurring.  In the citizen science community, this is how forward progress is made…eventually.

https://dna-explained.com/2014/09/25/ancient-dna-matches-what-do-they-mean/

https://dna-explained.com/2014/09/30/ancient-dna-matching-a-cautionary-tale/

More ancient DNA samples for comparison:

https://dna-explained.com/2014/10/04/more-ancient-dna-samples-for-comparison/

A Siberian sample that also matches the Malta Child whose remains were analyzed in late 2013.

https://dna-explained.com/2014/11/12/kostenki14-a-new-ancient-siberian-dna-sample/

Felix has prepared a list of kits that he has processed, along with their GedMatch numbers and other relevant information, like gender, haplogroup(s), age and location of sample.

http://www.y-str.org/p/ancient-dna.html

Furthermore, in a collaborative effort with Family Tree DNA, Felix formed an Ancient DNA project and uploaded the ancient autosomal files.  This is the first time that consumers can match with Ancient kits within the vendor’s data bases.

https://www.familytreedna.com/public/Ancient_DNA

Recently, GedMatch added a composite Archaic DNA Match comparison tool where your kit number is compared against all of the ancient DNA kits available.  The output is a heat map showing which samples you match most closely.

gedmatch ancient heat map

Indeed, it has been a banner year for ancient DNA and making additional discoveries about DNA and our ancestors.  Thank you Felix.

Haplogroup Definition

That SNP tsunami that we discussed last year…well, it made landfall this year and it has been storming all year long…in a good way.  At least, ultimately, it will be a good thing.  If you asked the haplogroup administrators today about that, they would probably be too tired to answer – as they’ve been quite overwhelmed with results.

The Big Y testing has been fantastically successful.  This is not from a Family Tree DNA perspective, but from a genetic genealogy perspective.  Branches have been being added to and sawed off of the haplotree on a daily basis.  This forced the renaming of the haplogroups from the old traditional R1b1a2 to R-M269 in 2012.  While there was some whimpering then, it would be nothing like the outright wailing now that would be occurring as haplogroup named reached 20 or so digits.

Alice Fairhurst discussed the SNP tsunami at the DNA Conference in Houston in October and I’m sure that the pace hasn’t slowed any between now and then.  According to Alice, in early 2014, there were 4115 individual SNPs on the ISOGG Tree, and as of the conference, there were 14,238 SNPs, with the 2014 addition total at that time standing at 10,213.  That is over 1000 per month or about 35 per day, every day.

Yes, indeed, that is the definition of a tsunami.  Every one of those additions requires one of a number of volunteers, generally haplogroup project administrators to evaluate the various Big Y results, the SNPs and novel variants included, where they need to be inserted in the tree and if branches need to be rearranged.  In some cases, naming request for previously unknown SNPs also need to be submitted.  This is all done behind the scenes and it’s not trivial.

The project I’m closest to is the R1b L-21 project because my Estes males fall into that group.  We’ve tested several, and I’ll be writing an article as soon as the final test is back.

The tree has grown unbelievably in this past year just within the L21 group.  This project includes over 700 individuals who have taken the Big Y test and shared their results which has defined about 440 branches of the L21 tree.  Currently there are almost 800 kits available if you count the ones on order and the 20 or so from another vendor.

Here is the L21 tree in January of 2014

L21 Jan 2014 crop

Compare this with today’s tree, below.

L21 dec 2014

Michael Walsh, Richard Stevens, David Stedman need to be commended for their incredible work in the R-L21 project.  Other administrators are doing equivalent work in other haplogroup projects as well.  I big thank you to everyone.  We’d be lost without you!

One of the results of this onslaught of information is that there have been fewer and fewer academic papers about haplogroups in the past few years.  In essence, by the time a paper can make it through the peer review cycle and into publication, the data in the paper is often already outdated relative to the Y chromosome.  Recently a new paper was released about haplogroup C3*.  While the data is quite valid, the authors didn’t utilize the new SNP naming nomenclature.  Before writing about the topic, I had to translate into SNPese.  Fortunately, C3* has been relatively stable.

https://dna-explained.com/2014/12/23/haplogroup-c3-previously-believed-east-asian-haplogroup-is-proven-native-american/

10th Annual International Conference on Genetic Genealogy

The Family Tree DNA International Conference on Genetic Genealogy for project administrators is always wonderful, but this year was special because it was the 10th annual.  And yes, it was my 10th year attending as well.  In all these years, I had never had a photo with both Max and Bennett.  Everyone is always so busy at the conferences.  Getting any 3 people, especially those two, in the same place at the same time takes something just short of a miracle.

roberta, max and bennett

Ten years ago, it was the first genetic genealogy conference ever held, and was the only place to obtain genetic genealogy education outside of the rootsweb genealogy DNA list, which is still in existence today.  Family Tree DNA always has a nice blend of sessions.  I always particularly appreciate the scientific sessions because those topics generally aren’t covered elsewhere.

https://dna-explained.com/2014/10/11/tenth-annual-family-tree-dna-conference-opening-reception/

https://dna-explained.com/2014/10/12/tenth-annual-family-tree-dna-conference-day-2/

https://dna-explained.com/2014/10/13/tenth-annual-family-tree-dna-conference-day-3/

https://dna-explained.com/2014/10/15/tenth-annual-family-tree-dna-conference-wrapup/

Jennifer Zinck wrote great recaps of each session and the ISOGG meeting.

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy/

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy-isogg-meeting/

http://www.ancestorcentral.com/decennial-conference-on-genetic-genealogy-sunday/

I thank Family Tree DNA for sponsoring all 10 conferences and continuing the tradition.  It’s really an amazing feat when you consider that 15 years ago, this industry didn’t exist at all and wouldn’t exist today if not for Max and Bennett.

Education

Two educational venues offered classes for genetic genealogists and have made their presentations available either for free or very reasonably.  One of the problems with genetic genealogy is that the field is so fast moving that last year’s session, unless it’s the very basics, is probably out of date today.  That’s the good news and the bad news.

https://dna-explained.com/2014/11/12/genetic-genealogy-ireland-2014-presentations 

https://dna-explained.com/2014/09/26/educational-videos-from-international-genetic-genealogy-conference-now-available/

In addition, three books have been released in 2014.emily book

In January, Emily Aulicino released Genetic Genealogy, The Basics and Beyond.

richard hill book

In October, Richard Hill released “Guide to DNA Testing: How to Identify Ancestors, Confirm Relationships and Measure Ethnicity through DNA Testing.”

david dowell book

Most recently, David Dowell’s new book, NextGen Genealogy: The DNA Connection was released right after Thanksgiving.

 

Ancestor Reconstruction – Raising the Dead

This seems to be the year that genetic genealogists are beginning to reconstruct their ancestors (on paper, not in the flesh) based on the DNA that the ancestors passed on to various descendants.  Those segments are “gathered up” and reassembled in a virtual ancestor.

I utilized Kitty Cooper’s tool to do just that.

https://dna-explained.com/2014/10/03/ancestor-reconstruction/

henry bolton probablyI know it doesn’t look like much yet but this is what I’ve been able to gather of Henry Bolton, my great-great-great-grandfather.

Kitty did it herself too.

http://blog.kittycooper.com/2014/08/mapping-an-ancestral-couple-a-backwards-use-of-my-segment-mapper/

http://blog.kittycooper.com/2014/09/segment-mapper-tool-improvements-another-wold-dna-map/

Ancestry.com wrote a paper about the fact that they have figured out how to do this as well in a research environment.

http://corporate.ancestry.com/press/press-releases/2014/12/ancestrydna-reconstructs-partial-genome-of-person-living-200-years-ago/

http://www.thegeneticgenealogist.com/2014/12/16/ancestrydna-recreates-portions-genome-david-speegle-two-wives/

GedMatch has created a tool called, appropriately, Lazarus that does the same thing, gathers up the DNA of your ancestor from their descendants and reassembles it into a DNA kit.

Blaine Bettinger has been working with and writing about his experiences with Lazarus.

http://www.thegeneticgenealogist.com/2014/10/20/finally-gedmatch-announces-monetization-strategy-way-raise-dead/

http://www.thegeneticgenealogist.com/2014/12/09/recreating-grandmothers-genome-part-1/

http://www.thegeneticgenealogist.com/2014/12/14/recreating-grandmothers-genome-part-2/

Tools

Speaking of tools, we have some new tools that have been introduced this year as well.

Genome Mate is a desktop tool used to organize data collected by researching DNA comparsions and aids in identifying common ancestors.  I have not used this tool, but there are others who are quite satisfied.  It does require Microsoft Silverlight be installed on your desktop.

The Autosomal DNA Segment Analyzer is available through www.dnagedcom.com and is a tool that I have used and found very helpful.  It assists you by visually grouping your matches, by chromosome, and who you match in common with.

adsa cluster 1

Charting Companion from Progeny Software, another tool I use, allows you to colorize and print or create pdf files that includes X chromosome groupings.  This greatly facilitates seeing how the X is passed through your ancestors to you and your parents.

x fan

WikiTree is a free resource for genealogists to be able to sort through relationships involving pedigree charts.  In November, they announced Relationship Finder.

Probably the best example I can show of how WikiTree has utilized DNA is using the results of King Richard III.

wiki richard

By clicking on the DNA icon, you see the following:

wiki richard 2

And then Richard’s Y, mitochondrial and X chromosome paths.

wiki richard 3

Since Richard had no descendants, to see how descendants work, click on his mother, Cecily of York’s DNA descendants and you’re shown up to 10 generations.

wiki richard 4

While this isn’t terribly useful for Cecily of York who lived and died in the 1400s, it would be incredibly useful for finding mitochondrial descendants of my ancestor born in 1802 in Virginia.  I’d love to prove she is the daughter of a specific set of parents by comparing her DNA with that of a proven daughter of those parents!  Maybe I’ll see if I can find her parents at WikiTree.

Kitty Cooper’s blog talks about additional tools.  I have used Kitty’s Chromosome mapping tools as discussed in ancestor reconstruction.

Felix Chandrakumar has created a number of fun tools as well.  Take a look.  I have not used most of these tools, but there are several I’ll be playing with shortly.

Exits and Entrances

With very little fanfare, deCODEme discontinued their consumer testing and reminded people to download their date before year end.

https://dna-explained.com/2014/09/30/decodeme-consumer-tests-discontinued/

I find this unfortunate because at one time, deCODEme seemed like a company full of promise for genetic genealogy.  They failed to take the rope and run.

On a sad note, Lucas Martin who founded DNA Tribes unexpectedly passed away in the fall.  DNA Tribes has been a long-time player in the ethnicity field of genetic genealogy.  I have often wondered if Lucas Martin was a pseudonym, as very little information about Lucas was available, even from Lucas himself.  Neither did I find an obituary.  Regardless, it’s sad to see someone with whom the community has worked for years pass away.  The website says that they expect to resume offering services in January 2015. I would be cautious about ordering until the structure of the new company is understood.

http://www.dnatribes.com/

In the last month, a new offering has become available that may be trying to piggyback on the name and feel of DNA Tribes, but I’m very hesitant to provide a link until it can be determined if this is legitimate or bogus.  If it’s legitimate, I’ll be writing about it in the future.

However, the big news exit was Ancestry’s exit from the Y and mtDNA testing arena.  We suspected this would happen when they stopped selling kits, but we NEVER expected that they would destroy the existing data bases, especially since they maintain the Sorenson data base as part of their agreement when they obtained the Sorenson data.

https://dna-explained.com/2014/10/02/ancestry-destroys-irreplaceable-dna-database/

The community is still hopeful that Ancestry may reverse that decision.

Ancestry – The Chromosome Browser War and DNA Circles

There has been an ongoing battle between Ancestry and the more seasoned or “hard-core” genetic genealogists for some time – actually for a long time.

The current and most long-standing issue is the lack of a chromosome browser, or any similar tools, that will allow genealogists to actually compare and confirm that their DNA match is genuine.  Ancestry maintains that we don’t need it, wouldn’t know how to use it, and that they have privacy concerns.

Other than their sessions and presentations, they had remained very quiet about this and not addressed it to the community as a whole, simply saying that they were building something better, a better mousetrap.

In the fall, Ancestry invited a small group of bloggers and educators to visit with them in an all-day meeting, which came to be called DNA Day.

https://dna-explained.com/2014/10/08/dna-day-with-ancestry/

In retrospect, I think that Ancestry perceived that they were going to have a huge public relations issue on their hands when they introduced their new feature called DNA Circles and in the process, people would lose approximately 80% of their current matches.  I think they were hopeful that if they could educate, or convince us, of the utility of their new phasing techniques and resulting DNA Circles feature that it would ease the pain of people’s loss in matches.

I am grateful that they reached out to the community.  Some very useful dialogue did occur between all participants.  However, to date, nothing more has happened nor have we received any additional updates after the release of Circles.

Time will tell.

https://dna-explained.com/2014/11/18/in-anticipation-of-ancestrys-better-mousetrap/

https://dna-explained.com/2014/11/19/ancestrys-better-mousetrap-dna-circles/

DNA Circles 12-29-2014

DNA Circles, while interesting and somewhat useful, is certainly NOT a replacement for a chromosome browser, nor is it a better mousetrap.

https://dna-explained.com/2014/11/30/chromosome-browser-war/

In fact, the first thing you have to do when you find a DNA Circle that you have not verified utilizing raw data and/or chromosome browser tools from either 23andMe, Family Tree DNA or Gedmatch, is to talk your matches into transferring their DNA to Family Tree DNA or download to Gedmatch, or both.

https://dna-explained.com/2014/11/27/sarah-hickerson-c1752-lost-ancestor-found-52-ancestors-48/

I might add that the great irony of finding the Hickerson DNA Circle that led me to confirm that ancestry utilizing both Family Tree DNA and GedMatch is that today, when I checked at Ancestry, the Hickerson DNA Circle is no longer listed.  So, I guess I’ve been somehow pruned from the circle.  I wonder if that is the same as being voted off of the island.  So, word to the wise…check your circles often…they change and not always in the upwards direction.

The Seamy Side – Lies, Snake Oil Salesmen and Bullys

Unfortunately a seamy side, an underbelly that’s rather ugly has developed in and around the genetic genealogy industry.  I guess this was to be expected with the rapid acceptance and increasing popularity of DNA testing, but it’s still very unfortunate.

Some of this I expected, but I didn’t expect it to be so…well…blatant.

I don’t watch late night TV, but I’m sure there are now DNA diets and DNA dating and just about anything else that could be sold with the allure of DNA attached to the title.

I googled to see if this was true, and it is, although I’m not about to click on any of those links.

google dna dating

google dna diet

Unfortunately, within the ever-growing genetic genealogy community a rather large rift has developed over the past couple of years.  Obviously everyone can’t get along, but this goes beyond that.  When someone disagrees, a group actively “stalks” the person, trying to cost them their employment, saying hate filled and untrue things and even going so far as to create a Facebook page titled “Against<personname>.”  That page has now been removed, but the fact that a group in the community found it acceptable to create something like that, and their friends joined, is remarkable, to say the least.  That was accompanied by death threats.

Bullying behavior like this does not make others feel particularly safe in expressing their opinions either and is not conducive to free and open discussion. As one of the law enforcement officers said, relative to the events, “This is not about genealogy.  I don’t know what it is about, yet, probably money, but it’s not about genealogy.”

Another phenomenon is that DNA is now a hot topic and is obviously “selling.”  Just this week, this report was published, and it is, as best we can tell, entirely untrue.

http://worldnewsdailyreport.com/usa-archaeologists-discover-remains-of-first-british-settlers-in-north-america/

There were several tip offs, like the city (Lanford) and county (Laurens County) is not in the state where it is attributed (it’s in SC not NC), and the name of the institution is incorrect (Johns Hopkins, not John Hopkins).  Additionally, if you google the name of the magazine, you’ll see that they specialize in tabloid “faux reporting.”  It also reads a lot like the King Richard genuine press release.

http://urbanlegends.about.com/od/Fake-News/tp/A-Guide-to-Fake-News-Websites.01.htm

Earlier this year, there was a bogus institutional site created as well.

On one of the DNA forums that I frequent, people often post links to articles they find that are relevant to DNA.  There was an interesting article, which has now been removed, correlating DNA results with latitude and altitude.  I thought to myself, I’ve never heard of that…how interesting.   Here’s part of what the article said:

Researchers at Aberdeen College’s Havering Centre for Genetic Research have discovered an important connection between our DNA and where our ancestors used to live.

Tiny sequence variations in the human genome sometimes called Single Nucleotide Polymorphisms (SNPs) occur with varying frequency in our DNA.  These have been studied for decades to understand the major migrations of large human populations.  Now Aberdeen College’s Dr. Miko Laerton and a team of scientists have developed pioneering research that shows that these differences in our DNA also reveal a detailed map of where our own ancestors lived going back thousands of years.

Dr. Laerton explains:  “Certain DNA sequence variations have always been important signposts in our understanding of human evolution because their ages can be estimated.  We’ve known for years that they occur most frequently in certain regions [of DNA], and that some alleles are more common to certain geographic or ethnic groups, but we have never fully understood the underlying reasons.  What our team found is that the variations in an individual’s DNA correlate with the latitudes and altitudes where their ancestors were living at the time that those genetic variations occurred.  We’re still working towards a complete understanding, but the knowledge that sequence variations are connected to latitude and altitude is a huge breakthrough by itself because those are enough to pinpoint where our ancestors lived at critical moments in history.”

The story goes on, but at the bottom, the traditional link to the publication journal is found.

The full study by Dr. Laerton and her team was published in the September issue of the Journal of Genetic Science.

I thought to myself, that’s odd, I’ve never heard of any of these people or this journal, and then I clicked to find this.

Aberdeen College bogus site

About that time, Debbie Kennett, DNA watchdog of the UK, posted this:

April Fools Day appears to have arrived early! There is no such institution as Aberdeen College founded in 1394. The University of Aberdeen in Scotland was founded in 1495 and is divided into three colleges: http://www.abdn.ac.uk/about/colleges-schools-institutes/colleges-53.php

The picture on the masthead of the “Aberdeen College” website looks very much like a photo of Aberdeen University. This fake news item seems to be the only live page on the Aberdeen College website. If you click on any other links, including the link to the so-called “Journal of Genetic Science”, you get a message that the website is experienced “unusually high traffic”. There appears to be no such journal anyway.

We also realized that Dr. Laerton, reversed, is “not real.”

I still have no idea why someone would invest the time and effort into the fake website emulating the University of Aberdeen, but I’m absolutely positive that their motives were not beneficial to any of us.

What is the take-away of all of this?  Be aware, very aware, skeptical and vigilant.  Stick with the mainstream vendors unless you realize you’re experimenting.

King Richard

King Richard III

The much anticipated and long-awaited DNA results on the remains of King Richard III became available with a very unexpected twist.  While the science team feels that they have positively identified the remains as those of Richard, the Y DNA of Richard and another group of men supposed to have been descended from a common ancestor with Richard carry DNA that does not match.

https://dna-explained.com/2014/12/09/henry-iii-king-of-england-fox-in-the-henhouse-52-ancestors-49/

https://dna-explained.com/2014/12/05/mitochondrial-dna-mutation-rates-and-common-ancestors/

Debbie Kennett wrote a great summary article.

http://cruwys.blogspot.com/2014/12/richard-iii-and-use-of-dna-as-evidence.html

More Alike than Different

One of the life lessons that genetic genealogy has held for me is that we are more closely related that we ever knew, to more people than we ever expected, and we are far more alike than different.  A recent paper recently published by 23andMe scientists documents that people’s ethnicity reflect the historic events that took place in the part of the country where their ancestors lived, such as slavery, the Trail of Tears and immigration from various worldwide locations.

23andMe European African map

From the 23andMe blog:

The study leverages samples of unprecedented size and precise estimates of ancestry to reveal the rate of ancestry mixing among American populations, and where it has occurred geographically:

  • All three groups – African Americans, European Americans and Latinos – have ancestry from Africa, Europe and the Americas.
  • Approximately 3.5 percent of European Americans have 1 percent or more African ancestry. Many of these European Americans who describe themselves as “white” may be unaware of their African ancestry since the African ancestor may be 5-10 generations in the past.
  • European Americans with African ancestry are found at much higher frequencies in southern states than in other parts of the US.

The ancestry proportions point to the different regional impacts of slavery, immigration, migration and colonization within the United States:

  • The highest levels of African ancestry among self-reported African Americans are found in southern states, especially South Carolina and Georgia.
  • One in every 20 African Americans carries Native American ancestry.
  • More than 14 percent of African Americans from Oklahoma carry at least 2 percent Native American ancestry, likely reflecting the Trail of Tears migration following the Indian Removal Act of 1830.
  • Among self-reported Latinos in the US, those from states in the southwest, especially from states bordering Mexico, have the highest levels of Native American ancestry.

http://news.sciencemag.org/biology/2014/12/genetic-study-reveals-surprising-ancestry-many-americans?utm_campaign=email-news-weekly&utm_source=eloqua

23andMe provides a very nice summary of the graphics in the article at this link:

http://blog.23andme.com/wp-content/uploads/2014/10/Bryc_ASHG2014_textboxes.pdf

The academic article can be found here:

http://www.cell.com/ajhg/home

2015

So what does 2015 hold? I don’t know, but I can’t wait to find out. Hopefully, it holds more ancestors, whether discovered through plain old paper research, cousin DNA testing or virtually raised from the dead!

What would my wish list look like?

  • More ancient genomes sequenced, including ones from North and South America.
  • Ancestor reconstruction on a large scale.
  • The haplotree becoming fleshed out and stable.
  • Big Y sequencing combined with STR panels for enhanced genealogical research.
  • Improved ethnicity reporting.
  • Mitochondrial DNA search by ancestor for descendants who have tested.
  • More tools, always more tools….
  • More time to use the tools!

Here’s wishing you an ancestor filled 2015!

 

Chromosome Browser War

There has been a lot of discussion lately, and I mean REALLY a lot, about chromosome browsers, the need or lack thereof, why, and what the information really means.

For the old timers in the field, we know the story, the reasons, and the backstory, but a lot of people don’t.  Not only are they only getting pieces of the puzzle, they’re confused about why there even is a puzzle.  I’ve been receiving very basic questions about this topic, so I thought I’d write an article about chromosome browsers, what they do for us, why we need them, how we use them and the three vendors, 23andMe, Ancestry and Family Tree DNA, who offer autosomal DNA products that provide a participant matching data base.

The Autosomal Goal

Autosomal DNA, which tests the part of your DNA that recombines between parents every generation, is utilized in genetic genealogy to do a couple of things.

  1. To confirm your connection to a specific ancestor through matches to other descendants.
  2. To break down genealogy brick walls.
  3. Determine ethnicity percentages which is not the topic of this article.

The same methodology is used for items 1 and 2.

In essence, to confirm that you share a common ancestor with someone, you need to either:

  1. Be a close relative – meaning you tested your mother and/or father and you match as expected. Or, you tested another known relative, like a first cousin, for example, and you also match as expected. These known relationships and matches become important in confirming or eliminating other matches and in mapping your own chromosomes to specific ancestors.
  2. A triangulated match to at least two others who share the same distant ancestor. This happens when you match other people whose tree indicates that you share a common ancestor, but they are not previously known to you as family.

Triangulation is the only way you can prove that you do indeed share a common ancestor with someone not previously identified as family.

In essence, triangulation is the process by which you match people who match you genetically with common ancestors through their pedigree charts.  I wrote about the process in this article “Triangulation for Autosomal DNA.”

To prove that you share a common ancestor with another individual, the DNA of  three proven descendants of that common ancestor must match at the same location.  I should add a little * to this and the small print would say, “ on relatively large segments.”  That little * is rather controversial, and we’ll talk about that in a little bit.  This leads us to the next step, which is if you’re a fourth person, and you match all three of those other people on that same segment, then you too share that common ancestor.  This is the process by which adoptees and those who are searching for the identity of a parent work through their matches to work forward in time from common ancestors to, hopefully, identify candidates for individuals who could be their parents.

Why do we need to do this?  Isn’t just matching our DNA and seeing a common ancestor in a pedigree chart with one person enough?  No, it isn’t.  I recently wrote about a situation where I had a match with someone and discovered that even though we didn’t know it, and still don’t know exactly how, we unquestionably share two different ancestral lines.

When you look at someone’s pedigree chart, you may see immediately that you share more than one ancestral line.  Your shared DNA could come from either line, both lines, or neither line – meaning from an unidentified common ancestor.  In genealogy parlance, those are known as brick walls!

Blaine Bettinger wrote about this scenario in his now classic article, “Everyone Has Two Family Trees – A Genealogical Tree and a Genetic Tree.”

Proving a Match

The only way to prove that you actually do share a genealogy relative with someone that is not a known family member is to triangulate.  This means searching other matches with the same ancestral surname, preferably finding someone with the same proven ancestral tree, and confirming that the three of you not only share matching DNA, but all three share the same matching DNA segments.  This means that you share the same ancestor.

Triangulation itself is a two-step process followed by a third step of mapping your own DNA so that you know where various segments came from.  The first two triangulation steps are discovering that you match other people on a common segment(s) and then determining if the matches also match each other on those same segments.

Both Family Tree DNA and 23andMe, as vendors have provided ways to do most of this.  www.gedmatch.com and www.dnagedcom.com both augment the vendor offerings.  Ancestry provides no tools of this type – which is, of course, what has precipitated the chromosome browser war.

Let’s look at how the vendors products work in actual practice.

Family Tree DNA

1. Chromosome browser – do they match you?

Family Tree DNA makes it easy to see who you match in common with someone else in their matching tool, by utilizing the ICW crossed X icon.

chromosome browser war13

In the above example, I am seeing who I match in common with my mother.  Sure enough, our three known cousins are the closest matches, shown below.

chromosome browser war14

You can then push up to 5 individuals through to the chromosome browser to see where they match the participant.

The following chromosome browser is an example of a 4 person match showing up on the Family Tree DNA chromosome browser.

This example shows known cousins matching.  But this is exactly the same scenario you’re looking for when you are matching previously unknown cousins – the exact same technique.

In this example, I am the participant, so these matches are matches to me and my chromosome is the background chromosome displayed.  I have switched from my mother’s side to known cousins on my father’s side.

chromosome browser war1

The chromosome browser shows that these three cousins all match the person whose chromosomes are being shown (me, in this case), but it doesn’t tell you if they also match each other.  With known cousins, it’s very unlikely (in my case) that someone would match me from my mother’s side, and someone from my father’s side, but when you’re working with unknown cousins, it’s certainly possible.  If your parents are from the same core population, like Germans or an endogamous population, you may well have people who match you on both sides of your family.  Simply put, you can’t assume they don’t.

It’s also possible that the match is a genuine genealogical match, but you don’t happen to match on the exact same segments, so the ancestor can’t yet be confirmed until more cousins sharing that same ancestral line are found who do match, and it’s possible that some segments could be IBS, identical by state, meaning matches by chance, especially small segments, below the match threshold.

2. Matrix – do they match each other?

Family Tree DNA also provides a tool called the Matrix where you can see if all of the people who match on the same segment, also match each other at some place on their DNA.

chromosome browser war2

The Matrix tool measures the same level of DNA as the default chromosome browser, so in the situation I’m using for an example, there is no issue.  However, if you drop the threshold of the match level, you may well, and in this case, you will, find matches well below the match threshold.  They are shown as matches because they have at least one segment above the match threshold.  If you don’t have at least one segment above the threshold, you’ll never see these smaller matches.  Just to show you what I mean, this is the same four people, above, with the threshold lowered to 1cM.  All those little confetti pieces of color are smaller matches.

chromosome browser war3

At Family Tree DNA, the match threshold is about 7cM.  Each of the vendors has a different threshold and a different way of calculating that threshold.

The only reason I mention this is because if you DON’T match with someone on the matrix, but you also show matches at smaller segments, understand that matrix is not reporting on those, so matrix matches are not negative proof, only positive indications – when you do match, both on the chromosome browser and utilizing the matrix tool.

What you do know at this point is that these individuals all match you on the same segments, and that they match each other someplace on their chromosomes, but what you don’t know is if they match each other on the same locations where they match you.

If you are lucky and your matches are cousins or experienced genetic genealogists and are willing to take a look at their accounts, they can tell you if they match the other people on the same segments where they match you – but that’s the only way to know unless they are willing to download their raw data file to GedMatch.  At GedMatch, you can adjust the match thresholds to any level you wish and you can compare one-to-one kits to see where any two kits who have provided you with their kit number match each other.

3. Downloading data – mapping your chromosome.

The “download to Excel” function at Family Tree DNA, located just above the chromosome browser graphic, on the left, provides you with the matching data of the individuals shown on the chromosome browser with their actual segment data shown. (The download button on the right downloads all of your matches, not just the ones shown in the browser comparison.)

The spreadsheet below shows the downloaded data for these four individuals.  You can see on chromosome 15 (yellow) there are three distinct segments that match (pink, yellow and blue,) which is exactly what is reflected on the graphic browser as well.

chromosome browser war4

On the spreadsheet below, I’ve highlighted, in red, the segments which appeared on the original chromosome browser – so these are only the matches at or over the match threshold.

chromosome browser war5

As you can see, there are 13 in total.

Smaller Segments

Up to this point, the process I’ve shared is widely accepted as the gold standard.

In the genetic genealogy community, there are very divergent opinions on how to treat segments below the match threshold, or below even 10cM.  Some people “throw them away,” in essence, disregard them entirely.  Before we look at a real life example, let’s talk about the challenges with small segments.

When smaller segments match, along with larger segments, I don’t delete them, throw them away, or disregard them.  I believe that they are tools and each one carries a message for us.  Those messages can be one of four things.

  1. This is a valid IBD, meaning identical by descent, match where the segment has been passed from one specific ancestor to all of the people who match and can be utilized as such.
  2. This is an IBS match, meaning identical by state, and is called that because we can’t yet identify the common ancestor, but there is one. So this is actually IBD but we can’t yet identify it as such. With more matches, we may well be able to identify it as IBD, but if we throw it away, we never get that chance. As larger data bases and more sophisticated software become available, these matches will fall into place.
  3. This is an IBS match that is a false match, meaning the DNA segments that we receive from our father and mother just happen to align in a way that matches another person. Generally these are relatively easy to determine because the people you match won’t match each other. You also won’t tend to match other people with the same ancestral line, so they will tend to look like lone outliers on your match spreadsheets, but not always.
  4. This is an IBS match that is population based. These are much more difficult to determine, because this is a segment that is found widely in a population. The key to determining these pileup areas, as discussed in the Ancestry article about their new phasing technique, if that you will find this same segment matching different proven lineages. This is the reason that Ancestry has implemented phasing – to identify and remove these match regions from your matches. Ancestry provided a graphic of my pileup areas, although they did not identify for me where on my chromosomes these pileup regions occurred. I do have some idea however, because I’ve found a couple of areas where I have matches from my mother’s side of the family from different ancestors – so these areas must be IBS on a population level. That does not, however, make them completely irrelevant.

genome pileups

The challenge, and problem, is where to make the cutoff when you’re eliminating match areas based on phased data.  For example, I lost all of my Acadian matches at Ancestry.  Of course, you would expect an endogamous population to share lots of the same DNA – and there are a huge number of Acadian descendants today – they are in fact a “population,” but those matches are (were) still useful to me.

I utilize Acadian matches from Family Tree DNA and 23andMe to label that part of my chromosome “Acadian” even if I can’t track it to a specific Acadian ancestor, yet.  I do know from which of my mother’s ancestors it originated, her great-grandfather, who is her Acadian ancestor.  Knowing that much is useful as well.

The same challenge exists for other endogamous groups – people with Jewish, Mennonite/Brethren/Amish, Native American and African American heritage searching for their mixed race roots arising from slavery.  In fact, I’d go so far as to say that this problem exists for anyone looking for ancestors beyond the 5th or 6th generation, because segments inherited from those ancestors, if there are any, will probably be small and fall below the generally accepted match thresholds.  The only way you will be able to find them, today, is the unlikely event that there is one larger segments, and it leads you on a search, like the case with Sarah Hickerson.

I want to be very clear – if you’re looking for only “sure thing” segments – then the larger the matching segment, the better the odds that it’s a sure thing, a positive, indisputable, noncontroversial match.  However, if you’re looking for ancestors in the distant past, in the 5th or 6th generation or further, you’re not likely to find sure thing matches and you’ll have to work with smaller segments. It’s certainly preferable and easier to work with large matches, but it’s not always possible.

In the Ralph and Coop paper, The Geography of Recent Genetic Ancestry Across Europe, they indicated that people who matched on segments of 10cM or larger were more likely to have a common ancestor with in the past 500 years.  Blocks of 4cM or larger were estimated to be from populations from 500-1500 years ago.  However, we also know that there are indeed sticky segments that get passed intact from generation to generation, and also that some segments don’t get divided in a generation, they simply disappear and aren’t passed on at all.  I wrote about this in my article titled, Generational Inheritance.

Another paper by Durand et al, Reducing pervasive false positive identical-by-descent segments detected by large-scale pedigree analysis, showed that 67% of the 2-4cM segments were false positives.  Conversely, that also means that 33% of the 2-4cM segments were legitimate IBD segments.

Part of the disagreement within the genetic genealogy community is based on a difference in goals.  People who are looking for the parents of adoptees are looking first and primarily as “sure thing” matches and the bigger the match segment, of course, the better because that means the people are related more closely in time.  For them, smaller segments really are useless.  However, for people who know their recent genealogy and are looking for those brick wall ancestors, several generations back in time, their only hope is utilizing those smaller segments.  This not black and white but shades of grey.  One size does not fit all.  Nor is what we know today the end of the line.  We learn every single day and many of our learning experiences are by working through our own unique genealogical situations – and sharing our discoveries.

On this next spreadsheet, you can see the smaller segments surrounding the larger segments – in other words, in the same match cluster – highlighted in green.  These are the segments that would be discarded as invalid if you were drawing the line at the match threshold.  Some people draw it even higher, at 10 cM.  I’m not being critical of their methodology or saying they are wrong.  It may well work best for them, but discarding small segments is not the only approach and other approaches do work, depending on the goals of the researcher.  I want my 33% IBD segments, thank you very much.

All of the segments highlighted in purple match between at least three cousins.  By checking the other cousins accounts, I can validate that they do all match each other as well, even though I can’t tell this through the Family Tree DNA matrix below the matching threshold.  So, I’ve proven these are valid.  We all received them from our common ancestor.

What about the white rows?  Are those valid matches, from a common ancestor?  We don’t have enough information to make that determination today.

chromosome browser war6

Downloading my data, and confirming segments to this common ancestor allows me to map my own chromosomes.  Now, I know that if someone matches me and any of these three cousins on chromosome 15, for example, between 33,335,760 and 58,455,135 – they are, whether they know it or not, descended from our common ancestral line.

In my opinion, I would think it a shame to discount or throw away all of these matches below 7cM, because you would be discounting 39 of your 52 total matches, or 75% of them.  I would be more conservative in assigning my segments with only one cousin match to any ancestor, but I would certainly note the match and hope that if I added other cousins, that segment would be eventually proven as IBD.

I used positively known cousins in this example because there is no disputing the validity of these matches.  They were known as cousins long before DNA testing.

Breaking Down Brick Walls

This is the same technique utilized to break down brick walls – and the more cousins you have tested, so that you can identify the maximum number of chromosome pieces of a particular ancestor – the better.

I used this same technique to identify Sarah Hickerson in my Thanksgiving Day article, utilizing these same cousins, plus several more.

Hey, just for fun, want to see what chromosome 15 looks like in this much larger sample???

In this case, we were trying to break down a brick wall.  We needed to determine if Sarah Hickerson was the mother of Elijah Vannoy.  All of the individuals in the left “Name” column are proven Vannoy cousins from Elijah, or in one case, William, from another child of Sarah Hickerson.  The individuals in the right “Match” column are everyone in the cousin match group plus the people in green who are Hickerson/Higginson descendants.  William, in green, is proven to descend from Sarah Hickerson and her husband, Daniel Vannoy.

chromosome browser war7

The first part of chromosome 15 doesn’t overlap with the rest.  Buster, David and I share another ancestral line as well, so the match in the non-red section of chromosome 15 may well be from that ancestral line.  It becomes an obvious possibility, because none of the people who share the Vannoy/Hickerson/Higginson DNA are in that small match group.

All of the red colored cells do overlap with at least one other individual in that group and together they form a cluster.  The yellow highlighted cells are the ones over the match threshold.  The 6 Hickerson/Higginson descendants are scattered throughout this match group.

And yes, for those who are going to ask, there are many more Vannoy/Hickerson triangulated groups.  This is just one of over 60 matching groups in total, some with matches well above the match threshold. But back to the chromosome browser wars!

23andMe

This example from 23andMe shows why it’s so very important to verify that your matches also match each other.

chromosome browser war8

Blue and purple match segments are to two of the same cousins that I used in the comparison at Family Tree DNA, who are from my father’s side.  Green is my first cousin from my mother’s side.   Note that on chromosome 11, they both match me on a common segment.  I know by working with them that they don’t match each other on that segment, so while they are both related to me, on chromosome 11, it’s not through the same ancestor.  One is from my father’s side and one is from my mother’s side.  If I hadn’t already known that, determining if they matched each other would be the acid test and would separate them into 2 groups.

23andMe provides you with a tool to see who your matches match that you match too.  That’s a tongue twister.

In essence, you can select any individual, meaning you or anyone that you match, on the left hand side of this tool, and compare them to any 5 other people that you match.  In my case above, I compared myself to my cousins, but if I want to know if my cousin on my mother’s side matches my two cousins on my father’s side, I simply select her name on the left and theirs on the right by using the drop down arrows.

chromosome browser war9

I would show you the results, but it’s in essence a blank chromosome browser screen, because she doesn’t match either of them, anyplace, which tells me, if I didn’t already know, that these two matches are from different sides of my family.

However, in other situations, where I match my cousin Daryl, for example, as well as several other people on the same segment, I want to know how many of these people Daryl matches as well.  I can enter Daryl’s name, with my name and their names in the group of 5, and compare.  23andMe facilitates the viewing or download of the results in a matrix as well, along with the segment data.  You can also download your entire list of matches by requesting aggregated data through the link at the bottom of the screen above or the bottom of the chromosome display.

I find it cumbersome to enter each matches name in the search tool and then enter all of the other matches names as well.  By utilizing the tools at www.dnagedcom.com, you can determine who your matches match as well, in common with you, in one spreadsheet.  Here’s an example.  Daryl in the chart below is my match, and this tool shows you who else she matches that I match as well, and the matching segments.  This allows me to correlate my match with Gwen for example, to Daryl’s match to Gwen to see if they are on the same segments.

chromosome browser war10

As you can see, Daryl and I both match Gwen on a common segment.  On my own chromosome mapping spreadsheet, I match several other people as well at that location, at other vendors, but so far, we haven’t been able to find any common genealogy.

Ancestry.com

At Ancestry.com, I have exactly the opposite problem.  I have lots of people I DNA match, and some with common genealogy, but no tools to prove the DNA match is to the common ancestor.

Hence, this is the crux of the chromosome browser wars.  I’ve just showed you how and why we use chromosome browsers and tools to show if our matches match each other in addition to us and on which segments.  I’ve also illustrated why.  Neither 23andMe nor Family Tree DNA provides perfect tools, which is why we utilize both GedMatch and DNAGedcom, but they do provide tools.  Ancestry provides no tools of this type.

At Ancestry, you have two kinds of genetic matches – ones without tree matches and ones with tree matches.  Pedigree matching is a service that Ancestry provides that the other vendors don’t.  Unfortunately, it also leads people to believe that because they match these people genetically and share a tree, that the tree shown is THE genetic match and it’s to the ancestor shown in the tree.  In fact, if the tree is wrong, either your tree or their tree, and you match them genetically, you will show up as a pedigree match as well.  Even if both pedigrees are right, that still doesn’t mean that your genetic match is through that ancestor.

How many bad trees are at Ancestry percentagewise?  I don’t know, but it’s a constant complaint and there is absolutely nothing Ancestry can do about it.  All they can do is utilize what they have, which is what their customers provide.  And I’m glad they do.  It does make the process of working through your matches much easier. It’s a starting point.  DNA matches with trees that also match your pedigree are shown with Ancestry’s infamous shakey leaf.

In fact, in my Sarah Hickerson article, it was a shakey leaf match that initially clued me that there was something afoot – maybe. I had to shift to another platform (Family Tree DNA) to prove the match however, where I had tools and lots of known cousins.

At Ancestry, I now have about 3000 matches in total, and of those, I have 33 shakey leaves – or people with whom I also share an ancestor in our pedigree charts.  A few of those are the same old known cousins, just as genealogy crazy as me, and they’ve tested at all 3 companies.

The fly in the ointment, right off the bat, is that I noticed in several of these matches that I ALSO share another ancestral line.

Now, the great news is that Ancestry shows you your surnames in common, and you can click on the surname and see the common individuals in both trees.

The bad news is that you have to notice and click to see that information, found in the lower left hand corner of this screen.

chromosome browser war11

In this case, Cook is an entirely different line, not connected to the McKee line shown.

However, in this next case, we have the same individual entered in our software, but differently.  It wasn’t close enough to connect as an ancestor, but close enough to note.  It turns out that Sarah Cook is the mother of Fairwick Claxton, but her middle name was not Helloms, nor was her maiden name, although that is a long-standing misconception that was proven incorrect with her husband’s War of 1812 documents many years ago. Unfortunately, this misinformation is very widespread in trees on the internet.

chromosome browser war12

Out of curiosity, and now I’m sorry I did this because it’s very disheartening – I looked to see what James Lee Claxton/Clarkson’s wife’s name was shown to be on the first page of Ancestry’s advanced search matches.

Despite extensive genealogical and DNA research, we don’t know who James Lee Claxton/Clarkson’s parents are, although we’ve disproven several possibilities, including the most popular candidate pre-DNA testing.  However, James’ wife was positively Sarah Cook, as given by her, along with her father’s name, and by witnesses to their marriage provided when she applied for a War of 1812 pension and bounty land.  I have the papers from the National Archives.

James Lee Claxton’s wife, Sara Cook is identified as follows in the first 50 Ancestry search entries.

Sarah Cook – 4

Incorrect entries:

  • Sarah Cook but with James’ parents listed – 3
  • Sarah Helloms Cook – 2, one with James’ parents
  • Sarah Hillhorns – 15
  • Sarah Cook Hitson – 13, some with various parents for James
  • No wife, but various parents listed for James – 12
  • No wife, no parents – 1

I’d much rather see no wife and no parents than incorrect information.

Judy Russell has expressed her concern about the effects of incorrect trees and DNA as well and we shared this concern with Ancestry during our meeting.

Ancestry themselves in their paper titled “Identifying groups of descendants using pedigrees and genetically inferred relationships in a large database” says, “”As with all analyses relating to DNA Circles™, tree quality is also an important caveat and limitation.”  So Ancestry is aware, but they are trying to leverage and utilize one of their biggest assets, their trees.

This brings us to DNA Circles.  I reviewed Ancestry’s new product release extensively in my Ancestry’s Better Mousetrap article.  To recap briefly, Ancestry gathers your DNA matches together, and then looks for common ancestors in trees that are public using an intelligent ranking algorithm that takes into account:

  1. The confidence that the match is due to recent genealogical history (versus a match due to older genealogical history or a false match entirely).
  2. The confidence that the identified common recent ancestor represents the same person in both online pedigrees.
  3. The confidence that the individuals have a match due to the shared ancestor in question as opposed to from another ancestor or from more distant genealogical history.

The key here is that Ancestry is looking for what they term “recent genealogical history.”  In their paper they define this as 10 generations, but the beta version of DNA Circles only looks back 7 generations today.  This was also reflected in their phasing paper, “Discovering IBD matches across a large, growing database.”

However, the unfortunate effect has been in many cases to eliminate matches, especially from endogamous groups.  By way of example, I lost my Acadian matches in the Ancestry new product release.  They would have been more than 7 generations back, and because they were endogamous, they may have “looked like” IBS segments, if IBS is defined at Ancestry as more than 7 or 10 generations back.  Hopefully Ancestry will tweek this algorithm in future releases.

Ancestry, according to their paper, “Identifying groups of descendants using pedigrees and genetically inferred relationships in a large database,” then clusters these remaining matching individuals together in Circles based on their pedigree charts.  You will match some of these people genetically, and some of them will not match you but will match each other.  Again, according to the paper, “these confidence levels are calculated by the direct-line pedigree size, the number of shared ancestral couples and the generational depth of the shared MRCA couple.”

Ancestry notes that, “using the concordance of two independent pieces of information, meaning pedigree relationships and patterns of match sharing among a set of individuals, DNA Circles can serve as supporting evidence for documented pedigree lines.”  Notice, Ancestry did NOT SAY proof.  Nothing that Ancestry provides in their DNA product constitutes proof.

Ancestry continues by saying that Circles “opens the possibility for people to identify distant relatives with whom they do not share DNA directly but with whom they still have genetic evidence supporting the relationship.”

In other words, Ancestry is being very clear in this paper, which is provided on the DNA Circles page for anyone with Circles, that they are giving you a tool, not “the answer,” but one more piece of information that you can consider as evidence.

joel vannoy circleJoel Vannoy circle2

You can see in my Joel Vannoy circle that I match both of these people both genetically and on their tree.

We, in the genetic genealogy community, need proof.  It certainly could be available, technically – because it is with other vendors and third party sites.

We need to be able to prove that our matches also match each other, and utilizing Ancestry’s tools, we can’t.  We also can’t do this at Ancestry by utilizing third party tools, so we’re in essence, stuck.

We can either choose to believe, without substantiation, that we indeed share a common ancestor because we share DNA segments with them plus a pedigree chart from that common ancestor, or we can initiate a conversation with our match that leads to either or both of the following questions:

  1. Have you or would you upload your raw data to GedMatch?
  2. Have you or would you upload your raw data file to Family Tree DNA?

Let the begging begin!!!

The Problem

In a nutshell, the problem is that even if your Ancestry matches do reply and do upload their file to either Family Tree DNA or GedMatch or both, you are losing most of the potential information available, or that would be available, if Ancestry provided a chromosome browser and matrix type tool.

In other words, you’d have to convince all of your matches and then they would have to convince all of the matches in the circle that they match and you don’t to upload their files.

Given that, of the 44 private tree shakey leaf matches that I sent messages to about 2 weeks ago, asking only for them to tell me the identity of our common pedigree ancestor, so far 2 only of them have replied, the odds of getting an entire group of people to upload files is infinitesimal.  You’d stand a better chance of winning the lottery.

One of the things Ancestry excels at is marketing.

ancestry ad1

If you’ve seen any of their ads, and they are everyplace, they focus on the “feel good” and they are certainly maximizing the warm fuzzy feelings at the holidays and missing those generations that have gone before us.

ancestry ad2

This is by no means a criticism, but it is why so many people do take the Ancestry DNA test. It’s advertised as easy and you’ll learn more about your family.  And you do, no question – you learn about your ethnicity and you get a list of DNA matches, pedigree matches when possible and DNA Circles.

The list of what you don’t get is every bit as important, a chromosome browser and tools to see whether your matches also match each other.  However, most of their customers will never know that.

Judging by the high percentage of inaccurate trees I found at Ancestry in my little experiment relative to the known and documented wife’s name of James Lee Claxton, which was 96%, based on just the first page of 50 search matches, it would appear that about 96% of Ancestry’s clientele are willing to believe something that someone else tells them without verification.  I doubt that it matters whether that information is a tree or a DNA test where they are shown  matches with common pedigree charts and circles.  I don’t mean this to be critical of those people.  We all began as novices and we need new people to become interested in both genealogy and DNA testing.

I suspect that most of Ancestry’s clients, especially new ones, simply don’t have a clue that there is a problem, let alone the magnitude and scope.  How would they?  They are just happy to find information about their ancestor.  And as someone said to me once – “but there are so many of those trees (with a wrong wife’s name), how can they all be wrong?”  Plus, the ads, at least some of them, certainly suggest that the DNA test grows your family tree for you.

ancestry ad3 signoff

The good news in all of this is that Ancestry’s widespread advertising has made DNA testing just part of the normal things that genealogists do.  Their marketing expertise along with recent television programs have served to bring DNA testing into the limelight. The bad news is that if people test at Ancestry instead of at a vendor who provides tools, we, and they, lose the opportunity to utilize those results to their fullest potential.  We, and they, lose any hope of proving an ancestor utilizing DNA.  And let’s face it, DNA testing and genealogy is about collaboration.  Having a DNA test that you don’t compare against others is pointless for genealogy purposes.

When a small group of bloggers and educators visited Ancestry in October, 2014, for what came to be called DNA Day, we discussed the chromosome browser and Ancestry’s plans for their new DNA Circles product, although it had not yet been named at that time.  I wrote about that meeting, including the fact that we discussed the need for a chromosome browser ad nauseum.  Needless to say, there was no agreement between the genetic genealogy community and the Ancestry folks.

When we discussed the situation with Ancestry they talked about privacy and those types of issues, which you can read about in detail in that article, but I suspect, strongly, that the real reason they aren’t keen on developing a chromosome browser lies in different areas.

  1. Ancestry truly believes that people cannot understand and utilize a chromosome browser and the information it provides. They believe that people who do have access to chromosome browsers are interpreting the results incorrectly today.
  2. They do not want to implement a complex feature for a small percentage of their users…the number bantered around informally was 5%…and I don’t know if that was an off-the-cuff number or based on market research. However, if you compare that number with the number of accurate versus inaccurate pedigree charts in my “James Claxton’s wife’s name” experiment, it’s very close…so I would say that the 5% number is probably close to accurate.
  3. They do not want to increase their support burden trying to explain the results of a chromosome browser to the other 95%. Keep in mind the number of users you’re discussing. They said in their paper they had 500,000 DNA participants. I think it’s well over 700,000 today, and they clearly expect to hit 1 million in 2015. So if you utilize a range – 5% of their users are 25,000-50,000 and 95% of their users are 475,000-950,000.
  4. Their clients have already paid their money for the test, as it is, and there is no financial incentive for Ancestry to invest in an add-on tool from which they generate no incremental revenue and do generate increased development and support costs. The only benefit to them is that we shut up!

So, the bottom line is that most of Ancestry’s clients don’t know or care about a chromosome browser.  There are, however, a very noisy group of us who do.

Many of Ancestry’s clients who purchase the DNA test do so as an impulse purchase with very little, if any, understanding of what they are purchasing, what it can or will do for them, at Ancestry or anyplace else, for that matter.

Any serious genealogist who researched the autosomal testing products would not make Ancestry their only purchase, especially if they could only purchase one test.  Many, if not most, serious genealogists have tested at all three companies in order to fish in different ponds and maximize their reach.  I suspect that most of Ancestry’s customers are looking for simple and immediate answers, not tools and additional work.

The flip side of that, however, if that we are very aware of what we, the genetic genealogy industry needs, and why, and how frustratingly lacking Ancestry’s product is.

Company Focus

It’s easy for us as extremely passionate and focused consumers to forget that all three companies are for-profit corporations.  Let’s take a brief look at their corporate focus, history and goals, because that tells a very big portion of the story.  Every company is responsible first and foremost to their shareholders and owners to be profitable, as profitable as possible which means striking the perfect balance of investment and expenditure with frugality.  In corporate America, everything has to be justified by ROI, or return on investment.

Family Tree DNA

Family Tree DNA was the first one of the companies to offer DNA testing and was formed in 1999 by Bennett Greenspan and Max Blankfeld, both still principles who run Family Tree DNA, now part of Gene by Gene, on a daily basis.  Family Tree DNA’s focus is only on genetic genealogy and they have a wide variety of products that produce a spectrum of information including various Y DNA tests, mitochondrial, autosomal, and genetic traits.  They are now the only commercial company to offer the Y STR and mitochondrial DNA tests, both very important tools for genetic genealogists, with a great deal of information to offer about our ancestors.

In April 2005, National Geographic’s Genographic project was announced in partnership with Family Tree DNA and IBM.  The Genographic project, was scheduled to last for 5 years, but is now in its 9th year.  Family Tree DNA and National Geographic announced Geno 2.0 in July of 2012 with a newly designed chip that would test more than 12,000 locations on the Y chromosome, in addition to providing other information to participants.

The Genographic project provided a huge boost to genetic genealogy because it provided assurance of legitimacy and brought DNA testing into the living room of every family who subscribed to National Geographic magazine.  Family Tree DNA’s partnership with National Geographic led to the tipping point where consumer DNA testing became mainstream.

In 2011 the founders expanded the company to include clinical genetics and a research arm by forming Gene by Gene.  This allowed them, among other things, to bring their testing in house by expanding their laboratory facilities.  They have continued to increase their product offerings to include sophisticated high end tests like the Big Y, introduced in 2013.

23andMe

23andMe is also privately held and began offering testing for medical and health information in November 2007, initially offering “estimates of predisposition for more than 90 traits ranging from baldness to blindness.”  Their corporate focus has always been in the medical field, with aggregated customer data being studied by 23andMe and other researchers for various purposes.

In 2009, 23andMe began to offer the autosomal test for genealogists, the first company to provide this service.  Even though, by today’s standards, it was very expensive, genetic genealogists flocked to take this test.

In 2013, after several years of back and forth with 23andMe ultimately failing to reply to the FDA, the FDA forced 23andMe to stop providing the medical results.  Clients purchasing the 23andMe autosomal product since November of 2013 receive only ethnicity results and the genealogical matching services.

In 2014, 23andMe has been plagued by public relations issues and has not upgraded significantly nor provided additional tools for the genetic genealogy community, although they recently formed a liaison with My Heritage.

23andMe is clearly focused on genetics, but not primarily genetic genealogy, and their corporate focus during this last year in particular has been, I suspect, on how to survive, given the FDA action.  If they steer clear of that landmine, I expect that we may see great things in the realm of personalized medicine from them in the future.

Genetic genealogy remains a way for them to attract people to increase their data base size for research purposes.  Right now, until they can again begin providing health information, genetic genealogists are the only people purchasing the test, although 23andMe may have other revenue sources from the research end of the business

Ancestry.com

Ancestry.com is a privately held company.  They were founded in the 1990s and have been through several ownership and organizational iterations, which you can read about in the wiki article about Ancestry.

During the last several years, Ancestry has purchased several other genealogy companies and is now the largest for-profit genealogy company in the world.  That’s either wonderful or terrible, depending on your experiences and perspective.

Ancestry has had an on-again-off-again relationship with DNA testing since 2002, with more than one foray into DNA testing and subsequent withdrawal from DNA testing.  If you are interested in the specifics, you can read about them in this article.

Ancestry’s goal, as it is with all companies, is profitability.  However, they have given themselves a very large black eye in the genetic genealogy community by doing things that we consider to be civically irresponsible, like destroying the Y and mitochondrial DNA data bases.  This still makes no sense, because while Ancestry spends money on one hand to acquire data bases and digitize existing records, on the other hand, they wiped out a data base containing tens of thousands of irreplaceable DNA records, which are genealogy records of a different type.  This was discussed at DNA Day and the genetic genealogy community retains hope that Ancestry is reconsidering their decision.

Ancestry has been plagued by a history of missteps and mediocrity in their DNA products, beginning with their Y and mitochondrial DNA products and continuing with their autosomal product.  Their first autosomal release included ethnicity results that gave many people very high percentages of Scandinavian heritage.  Ancestry never acknowledged a problem and defended their product to the end…until the day when they announced an update titled….a whole new you.  They are marketing geniuses.  While many people found their updated product much more realistic, not everyone was happy.  Judy Russell wrote a great summary of the situation.

It’s difficult, once a company has lost their credibility, for them to regain it.

I think Ancestry does a bang up job of what their primary corporate goal is….genealogy records and subscriptions for people to access those records. I’m a daily user.  Today, with their acquisitions, it would be very difficult to be a serious genealogist without an Ancestry subscription….which is of course what their corporate goal has been.

Ancestry does an outstanding job of making everything look and appear easy.  Their customer interface is intuitive and straightforward, for the most part. In fact, maybe they have made both genealogy and genetic genealogy look a little too easy.  I say this tongue in cheek, full well knowing that the ease of use is how they attract so many people, and those are the same people who ultimately purchase the DNA tests – but the expectation of swabbing and the answer appearing is becoming a problem.  I’m glad that Ancestry has brought DNA testing to so many people but this success makes tools like the chromosome browser/matrix that much more important – because there is so much genealogy information there just waiting to be revealed.  I also feel that their level of success and visibility also visits upon them the responsibility for transparency and accuracy in setting expectations properly – from the beginning – with the ads. DNA testing does not “grow your tree” while you’re away.

I’m guessing Ancestry entered the DNA market again because they saw a way to sell an additional product, autosomal DNA testing, that would tie people’s trees together and provide customers with an additional tool, at an additional price, and give them yet another reason to remain subscribed every year.  Nothing wrong with that either.  For the owners, a very reasonable tactic to harness a captive data base whose ear you already have.

But Ancestry’s focus or priority is not now, and never has been, quality, nor genetic genealogy.  Autosomal DNA testing is a tool for their clients, a revenue generation source for them, and that’s it.  Again, not a criticism.  Just the way it is.

In Summary

As I look at the corporate focus of the three players in this space, I see three companies who are indeed following their corporate focus and vision.  That’s not a bad thing, unless the genetic genealogy community focus finds itself in conflict with the results of their corporate focus.

It’s no wonder that Family Tree DNA sponsors events like the International DNA Conference and works hand in hand with genealogists and project administrators.  Their focus is and always has been genetic genealogy.

People do become very frustrated with Family Tree DNA from time to time, but just try to voice those frustrations to upper management at either 23andMe or Ancestry and see how far you get.  My last helpdesk query to 23andMe submitted on October 24th has yet to receive any reply.  At Family Tree DNA, I e-mailed the project administrator liaison today, the Saturday after Thanksgiving, hoping for a response on Monday – but I received one just a couple hours later – on a holiday weekend.

In terms of the chromosome browser war – and that war is between the genetic genealogy community and Ancestry.com, I completely understand both positions.

The genetic genealogy community has been persistent, noisy, and united.  Petitions have been created and signed and sent to Ancestry upper management.  To my knowledge, confirmation of any communications surrounding this topic with the exception of Ancestry reaching out to the blogging and education community, has never been received.

This lack of acknowledgement and/or action on the issues at hand frustrates the community terribly and causes reams of rather pointed and very direct replies to Anna Swayne and other Ancestry employees who are charged with interfacing with the public.  I actually feel sorry for Anna.  She is a very nice person.  If I were in her position, I’d certainly be looking for another job and letting someone else take the brunt of the dissatisfaction.  You can read her articles here.

I also understand why Ancestry is doing what they are doing – meaning their decision to not create a chromosome browser/match matrix tool.  It makes sense if you sit in their seat and now have to look at dealing with almost a million people who will wonder why they have to use a chromosome browser and or other tools when they expected their tree to grow while they were away.

I don’t like Ancestry’s position, even though I understand it, and I hope that we, as a community, can help justify the investment to Ancestry in some manner, because I fully believe that’s the only way we’ll ever get a chromosome browser/match matrix type tool.  There has to be a financial benefit to Ancestry to invest the dollars and time into that development, as opposed to something else.  It’s not like Ancestry has additional DNA products to sell to these people.  The consumers have already spent their money on the only DNA product Ancestry offers, so there is no incentive there.

As long as Ancestry’s typical customer doesn’t know or care, I doubt that development of a chromosome browser will happen unless we, as a community, can, respectfully, be loud enough, long enough, like an irritating burr in their underwear that just won’t go away.

burr

The Future

What we “know” and can do today with our genomes far surpasses what we could do or even dreamed we could do 10 years ago or even 5 or 2 years ago.  We learn everyday.

Yes, there are a few warts and issues to iron out.  I always hesitate to use words like “can’t,” “never” and “always” or to use other very strongly opinionated or inflexible words, because those words may well need to be eaten shortly.

There is so much more yet to be done, discovered and learned.  We need to keep open minds and be willing to “unlearn” what we think we knew when new and better information comes along.  That’s how scientific discovery works.  We are on the frontier, the leading edge and yes, sometimes the bleeding edge.  But what a wonderful place to be, to be able to contribute to discovery on a new frontier, our own genes and the keys to our ancestors held in our DNA.

2014 Y Tree Released by Family Tree DNA

On April 25th, DNA Day and Arbor Day, Family Tree DNA updated and released their 2014 Y haplotree created in partnership with the Genographic project.  This has been a massive project, expanding the tree from about 850 SNPs to over 6200, of which about 1200 are “terminal,” meaning the end of a branch, and the rest being proven to be duplicates.

If you’re a newbie, this would be a good place perhaps to read about what a haplogroup is and the new Y naming convention which replaces the well-known group names like R1b1a2 with the SNP shorthand version of the same haplogroup name, R-M269.  From this time forward, the haplogroups will be known by their SNP names and the longhand version is obsolete, although you will always see it in older documents, articles and papers.  In fact, this entire tree has been made possible by SNP testing by both academic organizations and consumers.  To understand the difference between regular STR marker testing and SNP testing, click here.

I’ve divided this article into two parts.  The first part is the “what did they do and why” part and the second is the “what does it mean to you” portion.

This tree update has been widely anticipated for some time now.  We knew that Family Tree DNA was calibrating the tree in partnership with the Genographic project, but we didn’t know what else would be included until the tree was released.

What Did Family Tree DNA Do, and Why?

Janine Cloud, the liaison at Family Tree DNA for Project Administrators has provided some information as to the big picture.

“First, we’re committed to the next iteration of the tree and it will be more comprehensive, but we’re going to be really careful about the data we use from other sources. It HAS to be from raw data, not interpreted data. Second, I’ve italicized what I think is really the mission statement for all the work that’s been done on this tree and that will be done in the future.”

Janine interviewed Elliott Greenspan of Family Tree DNA about the new tree, and here are some of the salient points from that discussion.

“This year we’re committing to launching another tree. This tree will be more comprehensive, utilizing data from external sources: known Sanger data, as well as data such as Big Y, and if we have direct access to the raw data to make the proof (from large companies, such as the Chromo2) or a publication, or something of that nature. That is our intention that it be added into the data.

We’re definitely committed to update at least once per year. Our intention is to use data from other sources, as well as any SNPs we can, but it must be well-vetted. NGS and SNP technology inherently has errors. You must curate for those errors otherwise you’re just putting slop out to customers. There are some SNPs that may bind to the X chromosome that you didn’t know. There are some low coverages that you didn’t know.

With technology such as this you’re able to overcome the urge to test only what you’re likely to be positive for, and instead use the shotgun method and test everything. This allows us to make the discovery that SNPs are not nearly as stable as we thought, and they have a larger potential use in that sense.

Not only does the raw data need to be vetted but it needs to make sense.  Using Geno 2.0, I only accepted samples that had the highest call rate, not just because it was the best quality but because it was the most data. I don’t want to be looking at data where I’m missing potential information A, or I may become confused by potential information B.  That is something that will bog us down. When you’re looking at large data sets, I’d much rather throw out 20% of them because they’re going to take 90% of the time than to do my best to get 1 extra SNP on the tree or 1 extra branch modified, that is not worth all of our time and effort. What is, is figuring out what the broader scope of people are, because that is how you break down origins. Figuring one single branch for one group of three people is not truly interesting until it’s 50 people, because 50 people is a population. Three people may be a family unit.  You have to have enough people to determine relevance. That’s why using large datasets and using complete datasets are very, very important.

I want it to be the most accurate tree it can be, but I also want it to be interesting. That’s the key. Historical relevance is what we’re to discover. Anthropological relevance. It’s not just who has the largest tree, it’s who can make the most sense out of what you have is important.”

Thanks to both Janine and Elliott for providing this information.

What is Provided in the Update?

The genetic genealogy community was hopeful that the new 2014 tree would be comprehensive, meaning that it would include not only the Genographic SNPs, but ones from Walk the Y, perhaps some Chromo2, Full Genomes results and the Big Y.  Perhaps we were being overly optimistic, especially given the huge influx of new SNPs, the SNP tsunami as we call it, over the past few months.  Family Tree DNA clearly had to put a stake in the sand and draw the line someplace.  So, what is actually included, how did they select the SNPs for the new tree and how does this integrate with the Genographic information?  This information was provided by Family Tree DNA.

Family Tree DNA created the 2014 Y-DNA Haplotree in partnership with the National Geographic Genographic Project using the proprietary GenoChip. Launched publicly in late 2012, the chip tests approximately 10,000 Y-DNA SNPs that had not, at the time, been phylogenetically classified.

The team used the first 50,000 male samples with the highest quality results to determine SNP positions. Using only tests with the highest possible “call rate” meant more available data, since those samples had the highest percentage of SNPs that produced results, or “calls.”

In some cases, SNPs that were on the 2010 Y-DNA Haplotree didn’t work well on the GenoChip, so the team used Sanger sequencing on anonymous samples to test those SNPs and to confirm ambiguous locations.

For example, if it wasn’t clear if a clade was a brother (parallel) clade, or a downstream clade, they tested for it.

The scope of the project did not include going farther than SNPs currently on the GenoChip in order to base the tree on the most data available at the time, with the cutoff for inclusion being about November of 2013.

Where data were clearly missing or underrepresented, the team curated additional data from the chip where it was available in later samples. For example, there were very few Haplogroup M samples in the original dataset of 50,000, so to ensure coverage, the team went through eligible Geno 2.0 samples submitted after November, 2013, to pull additional Haplogroup M data. That additional research was not necessary on, for example, the robust Haplogroup R dataset, for which they had a significant number of samples.

Family Tree DNA, again in partnership with the Genographic Project, is committed to releasing at least one update to the tree this year. The next iteration will be more comprehensive, including data from external sources such as known Sanger data, Big Y testing, and publications. If the team gets direct access to raw data from other large companies’ tests, then that information will be included as well. We are also committed to at least one update per year in the future.

Known SNPs will not intentionally be renamed. Their original names will be used since they represent the original discoverers of the SNP. If there are two names, one will be chosen to be displayed and the additional name will be available in the additional data, but the team is taking care not to make synonymous SNPs seems as if they are two separate SNPs. Some examples of that may exist initially, but as more SNPs are vetted, and as the team learns more, those examples will be removed.

In addition, positions or markers within STRs, as they are discovered, or large insertion/deletion events inside homopolymers, potentially may also be curated from additional data because the event cannot accurately be proven. A homopolymer is a sequence of identical bases, such as AAAAAAAAA or TTTTTTTTT. In such cases it’s impossible to tell which of the bases the insertion is, or if/where one was deleted. With technology such as Next Generation Sequencing, trying to get SNPs in regions such as STRs or homopolymers doesn’t make sense because we’re discovering non-ambiguous SNPs that define the same branches, so we can use the non-ambiguous SNPs instead.

Some SNPs from the 2010 tree have been intentionally removed. In some cases, those were SNPs for which the team never saw a positive result, so while it may be a legitimate SNP, even haplogroup defining, it was outside of the current scope of the tree. In other cases, the SNP was found in so many locations that it could cause the orientation of the tree to be drawn in more than one way. If the SNP could legitimately be positioned in more than one haplogroup, the team deemed that SNP to not be haplogroup defining, but rather a high polymorphic location.

To that end, SNPs no longer have .1, .2, or .3 designations. For example, J-L147.1 is simply J-L147, and I-147.2 is simply I-147.  Those SNPs are positioned in the same place, but back-end programming will assign the appropriate haplogroup using other available information such as additional SNPs tested or haplogroup origins listed. If other SNPs have been tested and can unambiguously prove the location of the multi-locus SNP for the sample, then that data is used. If not, matching haplogroup origin information is used.

We will also move to shorthand haplogroup designations exclusively. Since we’re committing to at least one iteration of the tree per year, using longhand that could change with each update would be too confusing.  For example, Haplogroup O used to have three branches: O1, O2, and O3. A SNP was discovered that combined O1 and O2, so they became O1a and O1b.

There are over 1200 branches on the 2014 Y Haplogroup tree, as compared to about 400 on the 2010 tree. Those branches contain over 6200 SNPs, so we’ve chosen to display select SNPs as “active” with an adjacent “More” button to show the synonymous SNPs if you choose.

In addition to the Family Tree DNA updates, any sample tested with the Genographic Project’s Geno 2.0 DNA Ancestry Kit, then transferred to FTDNA will automatically be re-synched on the Geno side. The Genographic Project is currently integrating the new data into their system and will announce on their website when the process is complete in the coming weeks.  At that time, all Geno 2.0 participants’ results will be updated accordingly and will be accessible via the Genographic Project website.

In summary:

  • Created in partnership with National Geographic’s Genographic Project
  • Used GenoChip containing ~10,000 previously unclassified Y-SNPs
  • Some of those SNPs came from Walk Through the Y and the 1000 Genome Project
  • Used first 50,000 high-quality male Geno 2.0 samples
  • Verified positions from 2010 YCC by Sanger sequencing additional anonymous samples
  • Filled in data on rare haplogroups using later Geno 2.0 samples

Statistics

  • Expanded from approximately 400 to over 1200 terminal branches
  • Increased from around 850 SNPs to over 6200 SNPs
  • Cut-off date for inclusion for most haplogroups was November 2013

Total number of SNPs broken down by haplogroup

A 406 DE 16 IJ 29 LT 12 P 81
B 69 E 1028 IJK 2 M 17 Q 198
BT 8 F 90 J 707 N 168 R 724
C 371 G 401 K 11 NO 16 S 5
CT 64 H 18 K(xLT) 1 O 936 T 148
D 208 I 455 L 129

myFTDNA Interface

  • Existing customers receive free update to predictions and confirmed branches based on existing SNP test results.
  • Haplogroup badge updated if new terminal branch is available
  • Updated haplotree design displays new SNPs and branches for your haplogroup
  • Branch names now listed in shorthand using terminal SNPs
  • For SNPs with more than one name, in most cases the original name for SNP was used, with synonymous SNPs listed when you click “More…”
  • No longer using SNP names with .1, .2, .3 suffixes. Back-end programming will place SNP in correct haplogroup using available data.
  • SNPs recommended for additional testing are pre-populated in the cart for your convenience. Just click to remove those you don’t want to test.
  • SNPs recommended for additional testing are based on 37-marker haplogroup origins data where possible, 25- or 12-marker data where 37 markers weren’t available.
  • Once you’ve tested additional SNPs, that information will be used to automatically recommend additional SNPs for you if they’re available.
  • If you remove those prepopulated SNPs from the cart, but want to re-add them, just refresh your page or close the page and return.
  • Only one SNP per branch can be ordered at one time – synonymous SNPs can possibly ordered from the Advanced Orders section on the Upgrade Order page.
  • Tests taken have moved to the bottom of the haplogroup page.

Coming attractions

  • Group Administrator Pages will have longhand removed.
  • At least one update to the tree to be released this year.
  • Update will include: data from Big Y, relevant publications, other companies’ tests from raw data.
  • We’ll set up a system for those who have tested with other big data companies to contribute their raw data file to future versions of the tree.
  • We’re committed to releasing at least one update per year.
  • The Genographic Project is currently integrating the new data into their system and will announce on their website when the process is complete in the coming weeks. At that time, all Geno 2.0 participants’ results will be updated accordingly and accessible via the Genographic Project website.

What Does This Mean to You?

Your Badge

On your welcome page, your badges are listed.  Your badge previously would have included the longhand form of the haplogroup, such as R1b1a2, but now it shows R-M269.

2014 y 1

Please note that badges are not yet showing on all participants pages.  If yours aren’t yet showing, clicking on the Haplotree and SNP page under the YDNA option on the blue options bar where your more detailed information is shown, below.

Your Haplogroup Name

Your haplogroup is now noted only as the SNP designation, R-M269, not the older longhand names.

2014 y 2 v2

Haplogroup R is a huge haplogroup, so you’ll need to scroll down to see your confirmed or predicted haplogroup, shown in green below.

2014 y 3

Redesigned Page

The redesigned haplotree page includes an option to order SNPs downstream of your confirmed or predicted haplogroup.  This refines your haplogroup and helps isolate your branch on the tree.  You may or may not want to do this.  In some cases, this does help your genealogy, especially in cases where you’re dealing with haplogroup R.  For the most part, haplogroups are more historical in nature.  For example, they will help you determine whether your ancestors are Native American, African, Anglo Saxon or maybe Viking.  Haplogroups help us reach back before the advent of surnames.

The new page shows which SNPs are available for you to order from the SNPs on the tree today, shown above, in blue to the right of the SNP branch.

SNPs not on the Tree

Not all known SNPs are on the tree.  Like I said, a line in the sand had to be drawn.  There are SNPs, many recently discovered, that are not on the tree.

To put this in perspective, the new tree incorporates 6200 SNPs (up from 850), but the Big Y “pool” of known SNPs against which Family Tree DNA is comparing those results was 36,562 when the first results were initially released at the end of February.

If you have taken advanced SNP testing, such as the Walk the Y, the Big Y, or tested individual SNPs, your terminal SNP may not be on the tree, which means that your terminal SNP shown on your page, such as R-M269 above, MAY NOT BE ACCURATE in light of that testing.  Why?  Because these newly discovered SNPs are not yet on the tree. This only affects people who have done advanced testing which means it does not affect most people.

Ordering SNPs

You can order relevant SNPs for your haplogroup on the tree by clicking on the “Add” button beside the SNP.

You can order SNPs not on the tree by clicking on the “Advanced Order Form” link available at the bottom of the haplotree page.

2014 y 4

If you’re not sure of what you want to do, or why, you might want to touch bases with your project administrators.  Depending on your testing goal, it might be much more advantageous, both scientifically and financially, for you to take either the Geno2 test or the Big Y.

At this point, in light of some of the issues with the new release, I would suggest maybe holding tight for a bit in terms of ordering new SNPs unless you’re positive that your haplogroup is correct and that the SNP selection you want to order would actually be beneficial to you.

Words of Caution

This are some bugs in this massive update.  You might want to check your haplogroup assignment to be sure it is reflected accurately based on any SNP testing you have had done, of course, excepting the very advanced tests mentioned above.

If you discover something that is inaccurate or questionable, please notify Family Tree DNA.  This is especially relevant for project administrators who are familiar with family groups and know that people who are in the same surname group should share a common base haplogroup, although some people who have taken further SNP testing will be shown with a downstream haplogroup, further down that particular branch of the tree.

What kind of result might you find suspicious or questionable?  For example, if in your surname project, your matching surname cousins are all listed at R-M269 and you were too previously, but now you’re suddenly in a different haplogroup, like E, there is clearly an error.

Any suspected or confirmed errors should be reported to Family Tree DNA.

They have made it very easy by providing a “Feedback” button on the top of the page and there is a “Y tree” option in the dropdown box.

2014 y 5

For administrators providing reports that involve more than one participant, please send to Groups@familytreedna.com and include the kit numbers, the participants names and the nature of the issue.

Additional Information

Family Tree DNA provides a free webinar that can be viewed about the 2014 Y Tree release.  You can see all of the webinars that are archived and available for viewing at:  https://www.familytreedna.com/learn/ftdna/webinars/

What’s Next?

The Genographic Project is in the process of updating to the same tree so their results can be synchronized with the 2014 tree.  A date for this has not yet been released.

Family Tree DNA has committed to at least one more update this year.

I know that this update was massive and required extensive reprogramming that affected almost every aspect of their webpage.  If you think about it, nearly every page had to be updated from the main page to the order page.  The tree is the backbone of everything.  I want to thank the Family Tree DNA and Genograpic combined team for their efforts and Bennett Greenspan for making sure this did happen, just as he committed to do in November at the last conference.

Like everyone else, I want everything NOW, not tomorrow.  We’re all passionate about this hobby – although I think it is more of a life mission for many – and surpassed hobby status long ago.

I know there are issues with the tree and they frustrate me, like everyone else.  Those issues will be resolved.  Family Tree DNA is actively working on reported issues and many have already been fixed.

There is some amount of disappointment in the genetic genealogy community about the SNPs not included on the tree, especially the SNPs recently discovered in advanced tests like the Big Y.  Other trees, like the ISOGG tree, do in fact reflect many of these newly discovered SNPs.

There are a couple of major differences.  First, ISOGG has an virtual army of volunteers who are focused on maintaining this tree.  We are all very lucky that they do, and that Alice Fairhurst coordinates this effort and has done so now for many years.  I would be lost without the ISOGG tree.

However, when a change is made to the ISOGG tree, and there have been thousands of changes, adds and moves over the years, nothing else is affected.  No one’s personal page, no one’s personal tree, no projects, no maps, no matches and no order pages.  ISOGG has no “responsibility” to anyone – in other words – it’s widely known and accepted that they are a volunteer organization without clients.

Family Tree DNA, on the other hand has half a million (or so) paying customers.  Tree changes have a huge domino ripple effect there – not only on their customers’ personal pages, but to their entire website, projects, support and orders.  A change at Family Tree DNA is much more significant than on the ISOGG page – not to mention – they don’t have the same army of volunteers and they have to rely on the raw science, not interpretation, as they said in the information they provided.  A tree update at Family Tree DNA is a very different animal than updating a stand-alone tree, especially considering their collaboration with various scientific organizations, including the National Geographic Society.

I commend Family Tree DNA for this update and thank them for the update and the educational materials.  I’m also glad to see that they do indeed rely only on science, not interpretation.  Frustrating to the genetic genealogist in me?  Sure.  But in the long run, it’s worth it to be sure the results are accurate.

Could this release have been smoother and more accurate?  Certainly.  Hopefully this is the big speed bump and future releases will be much more graceful.  It’s easy to see why there aren’t any other companies providing this type of comprehensive testing.  It’s gone from an easy 12 marker “do we match” scenario to the forefront of pioneering population genetics.  And all within a decade.  It’s amazing that any company can keep up.

 

2013’s Dynamic Dozen – Top Genetic Genealogy Happenings

dna 8 ball

Last year I wrote a column at the end of the year titled  “2012 Top 10 Genetic Genealogy Happenings.”  It’s amazing the changes in this industry in just one year.  It certainly makes me wonder what the landscape a year from now will look like.

I’ve done the same thing this year, except we have a dozen.  I couldn’t whittle it down to 10, partly because there has been so much more going on and so much change – or in the case of Ancestry, who is noteworthy because they had so little positive movement.

If I were to characterize this year of genetic genealogy, I would call it The Year of the SNP, because that applies to both Y DNA and autosomal.  Maybe I’d call it The Legal SNP, because it is also the year of law, court decisions, lawsuits and FDA intervention.  To say it has been interesting is like calling the Eiffel Tower an oversized coat hanger.

I’ll say one thing…it has kept those of us who work and play in this industry hopping busy!  I guarantee you, the words “I’m bored” have come out of the mouth of no one in this industry this past year.

I’ve put these events in what I consider to be relatively accurate order.  We could debate all day about whether the SNP Tsunami or the 23andMe mess is more important or relevant – and there would be lots of arguing points and counterpoints…see…I told you lawyers were involved….but in reality, we don’t know yet, and in the end….it doesn’t matter what order they are in on the list:)

Y Chromosome SNP Tsunami Begins

The SNP tsumani began as a ripple a few years ago with the introduction at Family Tree DNA of the Walk the Y program in 2007.  This was an intensively manual process of SNP discovery, but it was effective.

By the time that the Geno 2.0 chip was introduced in 2012, 12,000+ SNPs would be included on that chip, including many that were always presumed to be equivalent and not regularly tested.  However, the Nat Geo chip tested them and indeed, the Y tree became massively shuffled.  The resolution to this tree shuffling hasn’t yet come out in the wash.  Family Tree DNA can’t really update their Y tree until a publication comes out with the new tree defined.  That publication has been discussed and anticipated for some time now, but it has yet to materialize.  In the mean time, the volunteers who maintain the ISOGG tree are swamped, to say the least.

Another similar test is the Chromo2 introduced this year by Britain’s DNA which scans 15,000 SNPs, many of them S SNPs not on the tree nor academically published, adding to the difficulty of figuring out where they fit on the Y tree.  While there are some very happy campers with their Chromo2 results, there is also a great deal of sloppy science, reporting and interpretation of “facts” through this company.  Kind of like Jekyll and Hyde.  See the Sloppy Science section.

But Walk the Y, Chromo2 and Geno 2.0, are only the tip of the iceburg.  The new “full Y” sequencing tests brought into the marketspace quietly in early 2013 by Full Genomes and then with a bang by Family Tree DNA with the their Big Y in November promise to revolutionize what we know about the Y chromosome by discovering thousands of previously unknown SNPs.  This will in effect swamp the Y tree whose branches we thought were already pretty robust, with thousands and thousands of leaves.

In essence, the promise of the “fully” sequenced Y is that what we might term personal or family SNPs will make SNP testing as useful as STR testing and give us yet another genealogy tool with which to separate various lines of one genetic family and to ratchet down on the time that the most common recent ancestor lived.

https://dna-explained.com/2013/03/31/new-y-dna-haplogroup-naming-convention/

https://dna-explained.com/2013/11/10/family-tree-dna-announces-the-big-y/

https://dna-explained.com/2013/11/16/what-about-the-big-y/

http://www.yourgeneticgenealogist.com/2013/11/first-look-at-full-genomes-y-sequencing.html

http://cruwys.blogspot.com/2013/12/a-first-look-at-britainsdna-chromo-2-y.html

http://cruwys.blogspot.com/2013/11/yseqnet-new-company-offering-single-snp.html

http://cruwys.blogspot.com/2013/11/the-y-chromosome-sequence.html

http://cruwys.blogspot.com/2013/11/a-confusion-of-snps.html

http://cruwys.blogspot.com/2013/11/a-simplified-y-tree-and-common-standard.html

23andMe Comes Unraveled

The story of 23andMe began as the consummate American dotcom fairy tale, but sadly, has deteriorated into a saga with all of the components of a soap opera.  A wealthy wife starts what could be viewed as an upscale hobby business, followed by a messy divorce and a mystery run-in with the powerful overlording evil-step-mother FDA.  One of the founders of 23andMe is/was married to the founder of Google, so funding, at least initially wasn’t an issue, giving 23andMe the opportunity to make an unprecedented contribution in the genetic, health care and genetic genealogy world.

Another way of looking at this is that 23andMe is the epitome of the American Dream business, a startup, with altruism and good health, both thrown in for good measure, well intentioned, but poorly managed.  And as customers, be it for health or genealogy or both, we all bought into the altruistic “feel good” culture of helping find cures for dread diseases, like Parkinson’s, Alzheimer’s and cancer by contributing our DNA and responding to surveys.

The genetic genealogy community’s love affair with 23andMe began in 2009 when 23andMe started focusing on genealogy reporting for their tests, meaning cousin matches.  We, as a community, suddenly woke up and started ordering these tests in droves.  A few months later, Family Tree DNA also began offering this type of testing as well.  The defining difference being that 23andMe’s primary focus has always been on health and medical information with Family Tree DNA focused on genetic genealogy.  To 23andMe, the genetic genealogy community was an afterthought and genetic genealogy was just another marketing avenue to obtain more people for their health research data base.  For us, that wasn’t necessarily a bad thing.

For awhile, this love affair went along swimmingly, but then, in 2012, 23andMe obtained a patent for Parkinson’s Disease.  That act caused a lot of people to begin to question the corporate focus of 23andMe in the larger quagmire of the ethics of patenting genes as a whole.  Judy Russell, the Legal Genealogist, discussed this here.  It’s difficult to defend 23andMe’s Parkinson’s patent while flaying alive Myriad for their BRCA patent.  Was 23andMe really as altruistic as they would have us believe?

Personally, this event made me very nervous, but I withheld judgment.  But clearly, that was not the purpose for which I thought my DNA, and others, was being used.

But then came the Designer Baby patent in 2013.  This made me decidedly uncomfortable.  Yes, I know, some people said this really can’t be done, today, while others said that it’s being done anyway in some aspects…but the fact that this has been the corporate focus of 23andMe with their research, using our data, bothered me a great deal.  I have absolutely no issue with using this information to assure or select for healthy offspring – but I have a personal issue with technology to enable parents who would select a “beauty child,” one with blonde hair and blue eyes and who has the correct muscles to be a star athlete, or cheerleader, or whatever their vision of their as-yet-unconceived “perfect” child would be.  And clearly, based on 23andMe’s own patent submission, that is the focus of their patent.

Upon the issuance of the patent, 23andMe then said they have no intention of using it.  They did not say they won’t sell it.  This also makes absolutely no business sense, to focus valuable corporate resources on something you have no intention of using?  So either they weren’t being truthful, they lack effective management or they’ve changed their mind, but didn’t state such.

What came next, in late 2013 certainly points towards a lack of responsible management.

23andMe had been working with the FDA for approval the health and medical aspect of their product (which they were already providing to consumers prior to the November 22nd cease and desist order) for several years.  The FDA wants assurances that what 23andMe is telling consumers is accurate.  Based on the letter issued to 23andMe on November 22nd, and subsequent commentary, it appears that both entities were jointly working towards that common goal…until earlier this year when 23andMe mysteriously “somehow forgot” about the FDA, the information they owed them, their submissions, etc.  They also forgot their phone number and their e-mail addresses apparently as well, because the FDA said they had heard nothing from them in 6 months, which backdates to May of 2013.

It may be relevant that 23andMe added the executive position of President and filled it in June of 2013, and there was a lot of corporate housecleaning that went on at that time.  However, regardless of who got housecleaned, the responsibility for working with the FDA falls squarely on the shoulders of the founders, owners and executives of the company.  Period.  No excuses.  Something that critically important should be on the agenda of every executive management meeting.   Why?  In terms of corporate risk, this was obviously a very high risk item, perhaps the highest risk item, because the FDA can literally shut their doors and destroy them.  There is little they can do to control or affect the FDA situation, except to work with the FDA, meet deadlines and engender goodwill and a spirit of cooperation.  The risk of not doing that is exactly what happened.

It’s unknown at this time if 23andMe is really that corporately arrogant to think they could simply ignore the FDA, or blatantly corporately negligent or maybe simply corporately stupid, but they surely betrayed the trust and confidence of their customers by failing to meet their commitments with and to the FDA, or even communicate with them.  I mean, really, what were they thinking?

There has been an outpouring of sympathy for 23andme and negative backlash towards the FDA for their letter forcing 23andMe to stop selling their offending medical product, meaning the health portion of their testing.  However, in reality, the FDA was only meting out the consequences that 23andMe asked for.  My teenage kids knew this would happen.  If you do what you’re not supposed to….X, Y and Z will, or won’t, happen.  It’s called accountability.  Just ask my son about his prom….he remembers vividly.  Now why my kids, or 23andMe, would push an authority figure to that point, knowing full well the consequences, utterly mystifies me.  It did when my son was a teenager and it does with 23andMe as well.

Some people think that the FDA is trying to stand between consumers and their health information.  I don’t think so, at least not in this case.  Why I think that is because the FDA left the raw data files alone and they left the genetic genealogy aspect alone.  The FDA knows full well you can download your raw data and for $5 process it at a third party site, obtaining health related genetic information.  The difference is that Promethease is not interpreting any data for you, only providing information.

There is some good news in this and that is that from a genetic genealogy perspective, we seem to be safe, at least for now, from government interference with the testing that has been so productive for genetic genealogy.  The FDA had the perfect opportunity to squish us like a bug (thanks to the opening provided by 23andMe,) and they didn’t.

The really frustrating aspect of this is that 23andMe was a company who, with their deep pockets in Silicon Valley and other investors, could actually afford to wage a fight with the FDA, if need be.  The other companies who received the original 2010 FDA letter all went elsewhere and focused on something else.  But 23andMe didn’t, they decided to fight the fight, and we all supported their decision.  But they let us all down.  The fight they are fighting now is not the battle we anticipated, but one brought upon themselves by their own negligence.  This battle didn’t have to happen, and it may impair them financially to such a degree that if they need to fight the big fight, they won’t be able to.

Right now, 23andMe is selling their kits, but only as an ancestry product as they work through whatever process they are working through with the FDA.  Unfortunately, 23andMe is currently having some difficulties where the majority of matches are disappearing from some testers records.  In other cases, segments that previously matched are disappearing.  One would think, with their only revenue stream for now being the genetic genealogy marketspace that they would be wearing kid gloves and being extremely careful, but apparently not.  They might even consider making some of the changes and enhancements we’ve requested for so long that have fallen on deaf ears.

One thing is for sure, it will be extremely interesting to see where 23andMe is this time next year.  The soap opera continues.

I hope for the sake of all of the health consumers, both current and (potentially) future, that this dotcom fairy tale has a happy ending.

Also, see the Autosomal DNA Comes of Age section.

https://dna-explained.com/2013/10/05/23andme-patents-technology-for-designer-babies/

http://www.thegeneticgenealogist.com/2013/10/07/a-new-patent-for-23andme-creates-controversy/

https://dna-explained.com/2013/11/13/genomics-law-review-discusses-designing-children/

http://www.thegeneticgenealogist.com/2013/06/11/andy-page-fills-new-president-position-at-23andme/

https://dna-explained.com/2013/11/25/fda-orders-23andme-to-discontinue-testing/

https://dna-explained.com/2013/11/26/now-what-23andme-and-the-fda/

https://dna-explained.com/2013/12/06/23andme-suspends-health-related-genetic-tests/

http://www.legalgenealogist.com/blog/2013/11/26/fooling-with-fda/

Supreme Court Decision – Genes Can’t Be Patented – Followed by Lawsuits

In a landmark decision, the Supreme Court determined that genes cannot be patented.  Myriad Genetics held patents on two BRCA genes that predisposed people to cancer.  The cost for the tests through Myriad was about $3000.  Six hours after the Supreme Court decision, Gene By Gene announced that same test for $995.  Other firms followed suit, and all were subsequently sued by Myriad for patent infringement.  I was shocked by this, but as one of my lawyer friends clearly pointed out, you can sue anyone for anything.  Making it stick is yet another matter.  Many firms settle to avoid long and very expensive legal battles.  Clearly, this issue is not yet resolved, although one would think a Supreme Court decision would be pretty definitive.  It potentially won’t be settled for a long time.

https://dna-explained.com/2013/06/13/supreme-court-decision-genes-cant-be-patented/

http://www.legalgenealogist.com/blog/2013/06/14/our-dna-cant-be-patented/

https://dna-explained.com/2013/09/07/message-from-bennett-greenspan-free-my-genes/

http://www.thegeneticgenealogist.com/2013/06/13/new-press-release-from-dnatraits-regarding-the-supreme-courts-holding-in-myriad/

http://www.legalgenealogist.com/blog/2013/08/18/testing-firms-land-counterpunch/

http://www.legalgenealogist.com/blog/2013/07/11/myriad-sues-genetic-testing-firms/

Gene By Gene Steps Up, Ramps Up and Produces

As 23andMe comes unraveled and Ancestry languishes in its mediocrity, Gene by Gene, the parent company of Family Tree DNA has stepped up to the plate, committed to do “whatever it takes,” ramped up the staff both through hiring and acquisitions, and is producing results.  This is, indeed, a breath of fresh air for genetic genealogists, as well as a welcome relief.

https://dna-explained.com/2013/08/07/gene-by-gene-acquires-arpeggi/

https://dna-explained.com/2013/12/05/family-tree-dna-listens-and-acts/

https://dna-explained.com/2013/12/10/family-tree-dnas-family-finder-match-matrix-released/

http://www.haplogroup.org/ftdna-family-finder-matches-get-new-look/

http://www.haplogroup.org/ftdna-family-finder-new-look-2/

http://www.haplogroup.org/ftdna-family-finder-matches-new-look-3/

Autosomal DNA Comes of Age

Autosomal DNA testing and analysis has simply exploded this past year.  More and more people are testing, in part, because Ancestry.com has a captive audience in their subscription data base and more than a quarter million of those subscribers have purchased autosomal DNA tests.  That’s a good thing, in general, but there are some negative aspects relative to Ancestry, which are in the Ancestry section.

Another boon to autosomal testing was the 23andMe push to obtain a million records.  Of course, the operative word here is “was” but that may revive when the FDA issue is resolved.  One of the down sides to the 23andMe data base, aside from the fact that it’s not genealogist friendly, is that so many people, about 90%, don’t communicate.  They aren’t interested in genealogy.

A third factor is that Family Tree DNA has provided transfer ability for files from both 23andMe and Ancestry into their data base.

Fourth is the site, GedMatch, at www.gedmatch.com which provides additional matching and admixture tools and the ability to match below thresholds set by the testing companies.  This is sometimes critically important, especially when comparing to known cousins who just don’t happen to match at the higher thresholds, for example.  Unfortunately, not enough people know about GedMatch, or are willing to download their files.  Also unfortunate is that GedMatch has struggled for the past few months to keep up with the demand placed on their site and resources.

A great deal of time this year has been spent by those of us in the education aspect of genetic genealogy, in whatever our capacity, teaching about how to utilize autosomal results. It’s not necessarily straightforward.  For example, I wrote a 9 part series titled “The Autosomal Me” which detailed how to utilize chromosome mapping for finding minority ethnic admixture, which was, in my case, both Native and African American.

As the year ends, we have Family Tree DNA, 23andMe and Ancestry who offer the autosomal test which includes the relative-matching aspect.  Fortunately, we also have third party tools like www.GedMatch.com and www.DNAGedcom.com, without which we would be significantly hamstrung.  In the case of DNAGedcom, we would be unable to perform chromosome segment matching and triangulation with 23andMe data without Rob Warthen’s invaluable tool.

https://dna-explained.com/2013/06/21/triangulation-for-autosomal-dna/

https://dna-explained.com/2013/07/13/combining-tools-autosomal-plus-y-dna-mtdna-and-the-x-chromosome/

https://dna-explained.com/2013/07/26/family-tree-dna-levels-the-playing-field-sort-of/

https://dna-explained.com/2013/08/03/kitty-coopers-chromsome-mapping-tool-released/

https://dna-explained.com/2013/09/29/why-dont-i-match-my-cousin/

https://dna-explained.com/2013/10/03/family-tree-dna-updates-family-finder-and-adds-triangulation/

https://dna-explained.com/2013/10/21/why-are-my-predicted-cousin-relationships-wrong/

https://dna-explained.com/2013/12/05/family-tree-dna-listens-and-acts/

https://dna-explained.com/2013/12/09/chromosome-mapping-aka-ancestor-mapping/

https://dna-explained.com/2013/12/10/family-tree-dnas-family-finder-match-matrix-released/

https://dna-explained.com/2013/12/15/one-chromosome-two-sides-no-zipper-icw-and-the-matrix/

https://dna-explained.com/2013/06/02/the-autosomal-me-summary-and-pdf-file/

DNAGedcom – Indispensable Third Party Tool

While this tool, www.dnagedcom.com, falls into the Autosomal grouping, I have separated it out for individual mention because without this tool, the progress made this year in autosomal DNA ancestor and chromosomal mapping would have been impossible.  Family Tree DNA has always provided segment matching boundaries through their chromosome browser tool, but until recently, you could only download 5 matches at a time.  This is no longer the case, but for most of the year, Rob’s tool saved us massive amounts of time.

23andMe does not provide those chromosome boundaries, but utilizing Rob’s tool, you can obtain each of your matches in one download, and then you can obtain the list of who your matches match that is also on your match list by requesting each of those files separately.  Multiple steps?  Yes, but it’s the only way to obtain this information, and chromosome mapping without the segment data is impossible

A special hats off to Rob.  Please remember that Rob’s site is free, meaning it’s donation based.  So, please donate if you use the tool.

http://www.yourgeneticgenealogist.com/2013/01/brought-to-you-by-adoptiondna.html

I covered www.Gedmatch.com in the “Best of 2012” list, but they have struggled this year, beginning when Ancestry announced that raw data file downloads were available.  GedMatch consists of two individuals, volunteers, who are still struggling to keep up with the required processing and the tools.  They too are donation based, so don’t forget about them if you utilize their tools.

Ancestry – How Great Thou Aren’t

Ancestry is only on this list because of what they haven’t done.  When they initially introduced their autosomal product, they didn’t have any search capability, they didn’t have a chromosome browser and they didn’t have raw data file download capability, all of which their competitors had upon first release.  All they did have was a list of your matches, with their trees listed, with shakey leaves if you shared a common ancestor on your tree.  The implication, was, and is, of course, that if you have a DNA match and a shakey leaf, that IS your link, your genetic link, to each other.  Unfortunately, that is NOT the case, as CeCe Moore documented in her blog from Rootstech (starting just below the pictures) as an illustration of WHY we so desperately need a chromosome browser tool.

In a nutshell, Ancestry showed the wrong shakey leaf as the DNA connection – as proven by the fact that both of CeCe’s parents have tested at Ancestry and the shakey leaf person doesn’t match the requisite parent.  And there wasn’t just one, not two, but three instances of this.  What this means is, of course, that the DNA match and the shakey leaf match are entirely independent of each other.  In fact, you could have several common ancestors, but the DNA at any particular location comes only from one on either Mom or Dad’s side – any maybe not even the shakey leaf person.

So what Ancestry customers are receiving is a list of people they match and possible links, but most of them have no idea that this is the case, and blissfully believe they have found their genetic connection.  They have found a genealogical cousin, and it MIGHT be the genetic connection.  But then again, they could have found that cousin simply by searching for the same ancestor in Ancestry’s data base.  No DNA needed.

Ancestry has added a search feature, allowed raw data file downloads (thank you) and they have updated their ethnicity predictions.  The ethnicity predictions are certainly different, dramatically different, but equally as unrealistic.  See the Ethnicity Makeovers section for more on this.  The search function helps, but what we really need is the chromosome browser, which they have steadfastly avoided promising.  Instead, they have said that they will give us “something better,” but nothing has materialized.

I want to take this opportunity, to say, as loudly as possible, that TRUST ME IS NOT ACCEPTABLE in any way, shape or form when it comes to genetic matching.  I’m not sure what Ancestry has in mind by the way of “better,” but it if it’s anything like the mediocrity with which their existing DNA products have been rolled out, neither I nor any other serious genetic genealogist will be interested, satisfied or placated.

Regardless, it’s been nearly 2 years now.  Ancestry has the funds to do development.  They are not a small company.  This is obviously not a priority because they don’t need to develop this feature.  Why is this?  Because they can continue to sell tests and to give shakey leaves to customers, most of whom don’t understand the subtle “untruth” inherent in that leaf match – so are quite blissfully happy.

In years past, I worked in the computer industry when IBM was the Big Dog against whom everyone else competed.  I’m reminded of an old joke.  The IBM sales rep got married, and on his wedding night, he sat on the edge of the bed all night long regaling his bride in glorious detail with stories about just how good it was going to be….

You can sign a petition asking Ancestry to provide a chromosome browser here, and you can submit your request directly to Ancestry as well, although to date, this has not been effective.

The most frustrating aspect of this situation is that Ancestry, with their plethora of trees, savvy marketing and captive audience testers really was positioned to “do it right,” and hasn’t, at least not yet.  They seem to be more interested in selling kits and providing shakey leaves that are misleading in terms of what they mean than providing true tools.  One wonders if they are afraid that their customers will be “less happy” when they discover the truth and not developing a chromosome browser is a way to keep their customers blissfully in the dark.

https://dna-explained.com/2013/03/21/downloading-ancestrys-autosomal-dna-raw-data-file/

https://dna-explained.com/2013/03/24/ancestry-needs-another-push-chromosome-browser/

https://dna-explained.com/2013/10/17/ancestrys-updated-v2-ethnicity-summary/

http://www.thegeneticgenealogist.com/2013/06/21/new-search-features-at-ancestrydna-and-a-sneak-peek-at-new-ethnicity-estimates/

http://www.yourgeneticgenealogist.com/2013/03/ancestrydna-raw-data-and-rootstech.html

http://www.legalgenealogist.com/blog/2013/09/15/dna-disappointment/

http://www.legalgenealogist.com/blog/2013/09/13/ancestrydna-begins-rollout-of-update/

Ancient DNA

This has been a huge year for advances in sequencing ancient DNA, something once thought unachievable.  We have learned a great deal, and there are many more skeletal remains just begging to be sequenced.  One absolutely fascinating find is that all people not African (and some who are African through backmigration) carry Neanderthal and Denisovan DNA.  Just this week, evidence of yet another archaic hominid line has been found in Neanderthal DNA and on Christmas Day, yet another article stating that type 2 Diabetes found in Native Americans has roots in their Neanderthal ancestors. Wow!

Closer to home, by several thousand years is the suggestion that haplogroup R did not exist in Europe after the ice age, and only later, replaced most of the population which, for males, appears to have been primarily haplogroup G.  It will be very interesting as the data bases of fully sequenced skeletons are built and compared.  The history of our ancestors is held in those precious bones.

https://dna-explained.com/2013/01/10/decoding-and-rethinking-neanderthals/

https://dna-explained.com/2013/07/04/ancient-dna-analysis-from-canada/

https://dna-explained.com/2013/07/10/5500-year-old-grandmother-found-using-dna/

https://dna-explained.com/2013/10/25/ancestor-of-native-americans-in-asia-was-30-western-eurasian/

https://dna-explained.com/2013/11/12/2013-family-tree-dna-conference-day-2/

https://dna-explained.com/2013/11/22/native-american-gene-flow-europe-asia-and-the-americas/

https://dna-explained.com/2013/12/05/400000-year-old-dna-from-spain-sequenced/

http://www.thegeneticgenealogist.com/2013/10/16/identifying-otzi-the-icemans-relatives/

http://cruwys.blogspot.com/2013/12/recordings-of-royal-societys-ancient.html

http://cruwys.blogspot.com/2013/02/richard-iii-king-is-found.html

https://dna-explained.com/2013/12/22/sequencing-of-neanderthal-toe-bone-reveals-unknown-hominin-line/

https://dna-explained.com/2013/12/26/native-americans-neanderthal-and-denisova-admixture/

http://dienekes.blogspot.com/2013/12/ancient-dna-what-2013-has-brought.html

Sloppy Science and Sensationalist Reporting

Unfortunately, as DNA becomes more mainstream, it becomes a target for both sloppy science or intentional misinterpretation, and possibly both.  Unfortunately, without academic publication, we can’t see results or have the sense of security that comes from the peer review process, so we don’t know if the science and conclusions stand up to muster.

The race to the buck in some instances is the catalyst for this. In other cases, and not in the links below, some people intentionally skew interpretations and results in order to either fulfill their own belief agenda or to sell “products and services” that invariably report specific findings.

It’s equally as unfortunate that much of these misconstrued and sensationalized results are coming from a testing company that goes by the names of BritainsDNA, ScotlandsDNA, IrelandsDNA and YorkshiresDNA. It certainly does nothing for their credibility in the eyes of people who are familiar with the topics at hand, but it does garner a lot of press and probably sells a lot of kits to the unwary.

I hope they publish their findings so we can remove the “sloppy science” aspect of this.  Sensationalist reporting, while irritating, can be dealt with if the science is sound.  However, until the results are published in a peer-reviewed academic journal, we have no way of knowing.

Thankfully, Debbie Kennett has been keeping her thumb on this situation, occurring primarily in the British Isles.

https://dna-explained.com/2013/08/24/you-might-be-a-pict-if/

http://cruwys.blogspot.com/2013/12/the-british-genetic-muddle-by-alistair.html

http://cruwys.blogspot.com/2013/12/setting-record-straight-about-sara.html

http://cruwys.blogspot.com/2013/09/private-eye-on-britainsdna.html

http://cruwys.blogspot.com/2013/07/private-eye-on-prince-williams-indian.html

http://cruwys.blogspot.com/2013/06/britainsdna-times-and-prince-william.html

http://cruwys.blogspot.com/2013/03/sense-about-genealogical-dna-testing.html

http://cruwys.blogspot.com/2013/03/sense-about-genetic-ancestry-testing.html

Citizen Science is Coming of Age

Citizen science has been slowing coming of age over the past few years.  By this, I mean when citizen scientists work as part of a team on a significant discovery or paper.  Bill Hurst comes to mind with his work with Dr. Doron Behar on his paper, A Copernican Reassessment of the Human Mitochondrial DNA from its Root or what know as the RSRS model.  As the years have progressed, more and more discoveries have been made or assisted by citizen scientists, sometimes through our projects and other times through individual research.  JOGG, the Journal of Genetic Genealogy, which is currently on hiatus waiting for Dr. Turi King, the new editor, to become available, was a great avenue for peer reviewed publication.  Recently, research projects have been set up by citizen scientists, sometimes crowd-funded, for specific areas of research.  This is a very new aspect to scientific research, and one not before utilized.

The first paper below includes the Family Tree DNA Lab, Thomas and Astrid Krahn, then with Family Tree DNA and Bonnie Schrack, genetic genealogist and citizen scientist, along with Dr. Michael Hammer from the University of Arizona and others.

https://dna-explained.com/2013/03/26/family-tree-dna-research-center-facilitates-discovery-of-ancient-root-to-y-tree/

https://dna-explained.com/2013/04/10/diy-dna-analysis-genomeweb-and-citizen-scientist-2-0/

https://dna-explained.com/2013/06/27/big-news-probable-native-american-haplogroup-breakthrough/

https://dna-explained.com/2013/07/22/citizen-science-strikes-again-this-time-in-cameroon/

https://dna-explained.com/2013/11/30/native-american-haplogroups-q-c-and-the-big-y-test/

http://www.yourgeneticgenealogist.com/2013/03/citizen-science-helps-to-rewrite-y.html

Ethnicity Makeovers – Still Not Soup

Unfortunately, ethnicity percentages, as provided by the major testing companies still disappoint more than thrill, at least for those who have either tested at more than one lab or who pretty well know their ethnicity via an extensive pedigree chart.

Ancestry.com is by far the worse example, swinging like a pendulum from one extreme to the other.  But I have to hand it to them, their marketing is amazing.  When I signed in, about to discover that my results had literally almost reversed, I was greeted with the banner “a new you.”  Yea, a new me, based on Ancestry’s erroneous interpretation.  And by reversed, I’m serious.  I went from 80% British Isles to 6% and then from 0% Western Europe to 79%. So now, I have an old wrong one and a new wrong one – and indeed they are very different.  Of course, neither one is correct…..but those are just pesky details…

23andMe updated their ethnicity product this year as well, and fine tuned it yet another time.  My results at 23andMe are relatively accurate.  I saw very little change, but others saw more.  Some were pleased, some not.

The bottom line is that ethnicity tools are not well understood by consumers in terms of the timeframe that is being revealed, and it’s not consistent between vendors, nor are the results.  In some cases, they are flat out wrong, as with Ancestry, and can be proven.  This does not engender a great deal of confidence.  I only view these results as “interesting” or utilize them in very specific situations and then only using the individual admixture tools at www.Gedmatch.com on individual chromosome segments.

As Judy Russell says, “it’s not soup yet.”  That doesn’t mean it’s not interesting though, so long as you understand the difference between interesting and gospel.

https://dna-explained.com/2013/08/05/autosomal-dna-ancient-ancestors-ethnicity-and-the-dandelion/

https://dna-explained.com/2013/10/04/ethnicity-results-true-or-not/

http://www.legalgenealogist.com/blog/2013/09/15/dna-disappointment/

http://cruwys.blogspot.com/2013/09/my-updated-ethnicity-results-from.html?utm_source=feedburner&utm_medium=email&utm_campaign=Feed%3A+Cruwysnews+%28Cruwys+news%29

https://dna-explained.com/2013/10/17/ancestrys-updated-v2-ethnicity-summary/

https://dna-explained.com/2013/10/19/determining-ethnicity-percentages/

http://www.thegeneticgenealogist.com/2013/09/12/ancestrydna-launches-new-ethnicity-estimate/

http://cruwys.blogspot.com/2013/12/a-first-look-at-chromo-2-all-my.html

Genetic Genealogy Education Goes Mainstream

With the explosion of genetic genealogy testing, as one might expect, the demand for education, and in particular, basic education has exploded as well.

I’ve written a 101 series, Kelly Wheaton wrote a series of lessons and CeCe Moore did as well.  Recently Family Tree DNA has also sponsored a series of free Webinars.  I know that at least one book is in process and very near publication, hopefully right after the first of the year.  We saw several conferences this year that provided a focus on Genetic Genealogy and I know several are planned for 2014.  Genetic genealogy is going mainstream!!!  Let’s hope that 2014 is equally as successful and that all these folks asking for training and education become avid genetic genealogists.

https://dna-explained.com/2013/08/10/ngs-series-on-dna-basics-all-4-parts/

https://sites.google.com/site/wheatonsurname/home

http://www.yourgeneticgenealogist.com/2012/08/getting-started-in-dna-testing-for.html

https://dna-explained.com/2013/12/17/free-webinars-from-family-tree-dna/

http://www.thegeneticgenealogist.com/2013/06/09/the-first-dna-day-at-the-southern-california-genealogy-society-jamboree/

http://www.yourgeneticgenealogist.com/2013/06/the-first-ever-independent-genetic.html

http://cruwys.blogspot.com/2013/10/genetic-genealogy-comes-to-ireland.html

http://cruwys.blogspot.com/2013/03/wdytya-live-day-3-part-2-new-ancient.html

http://cruwys.blogspot.com/2013/03/who-do-you-think-you-are-live-day-3.html

http://cruwys.blogspot.com/2013/03/who-do-you-think-you-are-live-2013-days.html

http://genealem-geneticgenealogy.blogspot.com/2013/03/the-surnames-handbook-guide-to-family.html

http://www.isogg.org/wiki/Beginners%27_guides_to_genetic_genealogy

A Thank You in Closing

I want to close by taking a minute to thank the thousands of volunteers who make such a difference.  All of the project administrators at Family Tree DNA are volunteers, and according to their website, there are 7829 projects, all of which have at least one administrator, and many have multiple administrators.  In addition, everyone who answers questions on a list or board or on Facebook is a volunteer.  Many donate their time to coordinate events, groups, or moderate online facilities.  Many speak at events or for groups.  Many more write articles for publications from blogs to family newsletters.  Additionally, there are countless websites today that include DNA results…all created and run by volunteers, not the least of which is the ISOGG site with the invaluable ISOGG wiki.  Without our volunteer army, there would be no genetic genealogy community.  Thank you, one and all.

2013 has been a banner year, and 2014 holds a great deal of promise, even without any surprises.  And if there is one thing this industry is well known for….it’s surprises.  I can’t wait to see what 2014 has in store for us!!!  All I can say is hold on tight….

Gene by Gene Genomics Research Center Lab Tour

 ftdna inside sign cropped

Both before and after the 9th Annual Family Tree DNA International Conference for Genetic Genealogy this past weekend, Max Blankfeld and Bennett Greenspan were gracious enough to allow interested administrators to visit and tour their labs.  I’ve toured other DNA labs, but their lab has very cool leading edge equipment.  It was a wonderful treat to see it in action.

What I didn’t have was my “good” camera, so I’m sharing my iPhone photos.

I went on the last tour available and there were only a few of us, so it an excellent opportunity to see things up close and personal.

ftdna genomics research center

This lab is much larger than I expected.  Gene by Gene, in addition to doing all of the DNA processing for Family Tree DNA, DNA Traits and the National Geographic Genographic project, is doing a significant amount of processing for research institutions such as medical schools. While we were there, they were getting ready to prep to run a large order of several hundred exome samples.

But come along with me and you can see for yourself.  Bennett gave the tour personally.  The bad news is that you’re going to have to rely on my memory, because nothing was allowed in the lab other than our cameras.  This was to prevent contamination.

ftdna lisa footies

There are other contamination prevention methods as well.  Anyone with open toed shoes had to put on booties.  Here’s my friend Lisa, who comments periodically on my blog, suiting up for the tour.  Next, we were given lab coats to wear inside the facility which we then took off and left by the door, but inside the lab, as we left.

ftdna lisa lab coat

The first stop inside is where they prepare the kits for shipping to customers when an order is placed.  They purchase the empty vials, prepare the formula and fill and cap the vials, all automatically.

ftdna vials for kit

The “capping” process is the most interesting part and caused them the most consternation in trying to figure out the best way to do this.  Bennett said they worried about having a non-tethered lid that might be dropped by the customer, and contaminated, as it turns out, needlessly.

After the kits come back, all but one of the vials goes into storage, shown below, beside the lab, for future testing.  This environment does not have to be specially controlled outside of a normal office environment.

ftdna sample storage

The vial that gets opened for the testing undergoes a different process that begins with removing the DNA from the vial and mixing it with a chemical solution that shakes the DNA out of the cells.

ftdna lab

This is done overnight in a shaker machine.  Reminded me of a paint shaker.

ftdna shaker

Have you ever seen a custom $600,000 freezer with a robot to retrieve the frozen goods?  No?  Well, you’re about to.  If you have ever tested with Family Tree DNA and there is any DNA left in a vial that has been opened, it’s in this freezer which took the vendor 7 weeks to assemble on site.  Capacity is over 550,000 vials and it’s about half full currently.

After the DNA is shaken out of the cells, that mixture has to be handled differently.  It has been barcoded during the entire process and the prepared DNA mixture is then put into storage plates which are robotically stored.  This retrieval process is initiated when an order is received by the robotic software.  Keep in mind that the unit holds more samples than Family Tree DNA has today, in a very regulated deep freeze environment.  Depending on what this robotic arm is doing, meaning moving plates around or extracting a specific vial, it changes its own tool on the end of its arm.  It knows where every vial is in the freezer.  I must admit, my Mom who has been gone since 2006 has DNA there and it made me feel kind of funny to know I was visiting “her.” But my DNA is with hers, along with a whole lot of other family members, so I guess it’s just one big family reunion in there.

After the correct vial is retrieved and the DNA mixture is extracted, the liquid is put onto a “chip” for the autosomal testing.  The chip itself is about an inch by maybe 3 inches and holds 12 tests.

ftdna chip 12

The DNA is pipetted into the side and then it is wicked into the chip itself.

ftdna loading dna on chip

Here is a set of two chips loaded and ready to be processed.  This means that at total of 24 individual samples are being sequenced.   Notice the little grey square to the size of each larger grey square.  That tiny grey square is where the DNA mixture it placed and it’s wicked into the larger grey square for processing.  We asked how that is done and were told that the technique is part of Illumina’s trade secrets.

ftdna chip loaded

Gene by Gene owns several sequencing machines.  I know they have at least two Sanger sequencing machines and 4 different sizes and types of Illumina sequencing machines that run chip based tests like the Geno 2, the Family Finder and now the Big Y tests, in addition to the exome and full genome tests.  These machines are incredible given that they can run hundreds of tests at a time, which is also how they have dropped the test costs exponentially in the past few years.  Some equipment is optimized for running many samples but more slowly and some for running fewer samples but more quickly.

ftdna sequencer

After reading and being automatically scored, the DNA results are reported to the client.

At the end of the lab tour, just outside, is the Customer Service area where the Customer Service Reps work.  I’ll tell you what, they had their hands full this week and weekend with their regular call load, a conference and an office full of nosey and interested project administrators.

ftdna csr area

Of course, during the course of the day, I had to visit the restroom.  I’ve always loved Max and Bennett’s sense of humor.

ftdna men cropped

In case you don’t know, the Y chromosome is much smaller than the X, hence, the difference in the signs.

 ftdna women

Let’s just say that in light of their new product announcement, the “Big Y,” I did a bit of a structural modification for them:)

ftdna men big

Thanks again to Max and Bennett for their hospitality.

Jennifer Zinck also wrote about the Friday lab tour on her blog, Ancestor Central.

Supreme Court Decision – Genes Can’t Be Patented

In a victory for consumers, patients, researchers and women, the Supreme Court today returned a decision that human genes cannot be patented.

Their decision states that DNA ”is a product of nature and not patent eligible merely because it has been isolated.”

This case was a result of a suit against Myriad Genetics, a company that was granted patents for isolating two human genes, known as BRCA1 and BRCA2, both of which are well known breast cancer genes, recently brought to light by Angelina Jolie’s decision to have preventative mastectomys after both the gene and related breast cancer were found to be prevalent in her family.  Shortly after that decision and surgery, Jolie’s aunt died of breast cancer.

While companies cannot patent the genes themselves, they can develop treatments and hopefully, cures, and those can be patented.  Synthetic genes created are also eligible for patents.  Myriad wasn’t the only company to do this.  The government has issued patents to over 4000 genes to both companies and universities.

The patenting of genes made it impossible for other competing companies who could test for the gene technically to do so.  In other words, it artificially created a sole supplier situation where only one company could provide the test for that gene, and therefore could set the price wherever they wanted.  Jolie revealed that the cost of screening for those two genes alone was $3000, a cost prohibitive to many women.  However, the actual cost of the testing is significantly less.  I was wondering just how much less, then the answer arrived in my inbox.

I know that Gene by Gene, through its division, DNA Traits has the capability to offer this test and has been selling it internationally since 2012.  Bennett Greenspan, president of Gene by Gene has discussed this with me privately, and how terribly it pained him not to be able to do this testing to help people within the US.  Bennett shared some pretty profound thoughts about the unfair situation this created.

I was just getting ready to call Bennett, when less than 6 hours after the Supreme Court decision, I received an e-mail from Gene by Gene, which contained the answer – $995.  So the actual cost to the American consumer is only about one third to one quarter of what they were being charged as a result of the patent.

Today’s Supreme Court decision is truly a victory for patients, consumers, researchers, women and all US citizens.  Below is the content of the e-mail I received from Gene by Gene announcing the ability for DNATraits to sell the BRCA test in the US.

dnatraits brca

In effort to increase access to potentially lifesaving BRCA1 and BRCA2 tests, DNATraits can now offer tests for $995, a fraction of the cost of similar tests prior to the court decision

HOUSTON — Jun. 13, 2013 – Thanks to today’s U.S. Supreme Court decision opening the door to greater access to genetic medicine by American patients and their health care providers, testing for genes specifically linked to breast, ovarian and other cancers will now be more widely available and at a lower cost than ever before.

DNATraits, a division of Houston-based genomics and genetics testing company Gene By Gene, Ltd., announced today that it will offer testing for the BRCA1 and BRCA2 genes in the United States for $995.  Prior to today’s unanimous Supreme Court ruling, when exorbitant licensing fees kept DNATraits and others from offering BRCA gene tests in the United States, the cost for such tests was around $4,000.

“We’re pleased to make this important testing more widely available and accessible in the United States,” said Gene By Gene President Bennett Greenspan.  “Our highly automated CLIA-registered lab and efficient processes enable us to make genetic and genomic testing more affordable and accessible to more individuals, in the U.S. and worldwide.  And that’s our company’s mission, in a nutshell.”

The company’s announcement about the tests, which gained national attention when actress Angelina Jolie courageously revealed in May that being a BRCA1 carrier was among the factors in her decision to have a preventive double mastectomy, comes after today’s Supreme Court ruling in “Association For Molecular Pathology v. Myriad Genetics.”

“We commend the Supreme Court for opening the door to greater technological innovation and access to genetic tools that promise to save and improve the quality of human lives in the United States,” Greenspan added.  “It’s critical that as an industry we are able to continue to engage in healthy competition to drive down the costs of these tests – because as more individuals have access to and undergo them, the more information we’ll have about many serious diseases that eventually may lead to cures.”

DNATraits has processed testing for the BRCA1 and BRCA2 genes for individuals living outside the U.S. since 2012.  Those genes are processed using traditional Sanger DNA sequencing, which is considered the gold standard for DNA analysis, at the company’s Genomic Research Center in Houston, a CLIA-registered lab which has processed more than 5 million discrete DNA tests from more than 700,000 individuals and organizations globally.

In addition to the BRCA gene tests, DNATraits offers a pre-natal array that covers 111 population specific diseases, as well as other not population-specific diseases, like Duchene Muscular Dystrophy.

Customer Inquiries

Individuals interested in learning more about either the BRCA1 or BRCA2 tests should ask their doctors for more information.  They and their health care providers can also visit the company’s website, www.dnatraits.com, or call (713) 868-1438 for more information.

Navigating 23andMe for Genealogy

When I was young, there was a local woman who was extremely unhappy with her husband’s late night carousing.  He would come home “a bit tipsy” as well, and tried to sneak in unnoticed by leaving the lights off.  She was tired of it, so she got even, er, um, I mean, created a learning moment.

She rearranged all of the furniture and you had to walk through the living room to get to the bedroom.  About 3AM, she heard a huge crash.

Well, that’s what 23andMe did a few weeks ago.  I know they think they improved their website, but they didn’t.  And what they’ve done is cause a huge amount of work for those of us who assist others who have tested at 23andMe.  People can’t find the genealogy tools.  They both renamed them and relocated them and we didn’t even get any new features in the deal.  Where features were located wasn’t intuitive before, and they still aren’t, but now they are in different unintuitive places than they were before.  In other words, stumble, thump, crash – the lights are out and someone’s home.

So, as a matter of self-defense, I’m writing this blog about the basics of how to navigate the 23andMe site and how to utilize their genealogy tools.  It’s easy to miss opportunities if you don’t understand the nuances of their system, and they do have some great tools, by whatever name they call them.

We’re only interested in the genetic genealogy aspect, so we’re not discussing how to navigate the rest of their site.  Yes, there is more to the site than genealogy:)

The sign-on screen still looks the same.  After that, it’s all different.

First, remember that if you manage multiple kits, 23andMe decides which one is your default and you may not come up as “yourself.”  You can solve that by flying over your name in the upper right hand corner and then clicking on “switch profiles.”  I surely wish they would let you select and save your selection permanently.  You have to switch profiles every time you sign on.

Making Yourself Visible

The second thing you need to make sure of is that you ARE sharing, that people can see you.

Fly over the gear on the left hand side of the page at the top.  You’ll see the Settings option, click on that, then look through the options there, but specifically the “Privacy/Consent” tab.

nav 23andme gear

I’ve had people who could not figure out why they never received any invitations and their friends couldn’t find them, and it’s because their selections precluded sharing or did not allow people to search for them.

Here’s part of the Setting page, but you’ll want to review all of the information under your various settings tabs.

nav 23andme 1

The main page has several panel buttons across the top.  Not all are shown below.  The two we are going to be interested in are the “DNA Relatives” and the “Ancestry Composition.”

nav 23andme 2

If you want a quick overview of all of your genealogy information at 23andMe, you can click on the “My Ancestry Overview” button, but that’s not where the meat is – it’s  more like an appetizer.

nav 23andme 3

Here’s an example of the overview page.  Hint, the 4% Scandinavian showing is NOT your results, just the “cover page.”

Ancestry Composition – Ethnic Percentages

Click on Ancestry Composition.

You’ll see your own results in a circle chart.

nav 23andme 4

You can toggle the “standard” estimate to speculative or conservative in the drop down box at the upper right.  You can also change this circle to “chromosome view” which is really interesting.  The bar graph shows me that the two locations with identifiable Native American ancestry are found on my chromosomes 1 and 2.

nav 23andme 5

If you’ve been following my blog, you’ll know that I took this information and ran with it.  Here’s the link to “The Autosomal Me” series.

If you’re interested in taking this further and trying to identify your lines that match up with different ethnic admixtures, take a look at the series, especially Part 4, “The Autosomal Me, Testing Company Results.”  You’ll need to utilize some special download techniques and tools found outside of 23andMe, such as www.dnagedcom.com and you’ll also be utilizing www.gedmatch.com as well.  What 23andMe provides you in this category is just the beginning.

Finding Matches

There are four ways to find and select people at 23andMe to invite to share their DNA with you.  23andMe is different than Family Tree DNA.  At Family Tree DNA, you are testing FOR genealogy, nothing else, so when you sign your authorization and consent for comparison, it speaks only to genealogy data, not medical data.  So everyone at Family Tree DNA is sharing unless they specifically elect not to.  23andMe also provides health information and many who tested for health traits are not interested in genealogy, so in order to share any information at 23andMe, you must invite them to share and they must agree.

Of course, 23andMe shows you a thumbnail of who you match, but there are several ways to refine and be selective about this process.

Searching for Specific People

If you know who you want to invite to match, enter their e-mail address, their name, their surname or their nickname at 23andMe in the main site search box.  If they have allowed searching and have tested at 23andMe, a link to request sharing will be shown, similar to the screen below.

Finding People with Common Surnames

First of all, to find people whose surnames include those in your family tree as well, in the general site search box, type in the surname you’re hunting for. Let’s hope it’s not Smith.

nav 23andme 6

The results of that search in all categories on the 23andMe site are shown, and you can click on any of the categories for more information.  In my case, I see that there are more than 100 people whose information includes Estes.  I can click on any of the links that say “invite so-and-so” to invite them to share with me.  I always customize the message.  Many people don’t reply to “generic” messages that don’t say why someone is asking to compare.

nav 23andme 7

Finding Genetic Matches

To see whose DNA you match, click on Family and Friends, then on DNA Relatives.

nav 23andme 8

The first person on your list, is you.  This is a good sanity check to be sure you’re comparing the right profile and not your cousins when you thought it was your own.

nav 23andme 9

Next you’ll see your closest matches.  These folks I’m most closely related to are my “Blessed Cousin Circle” who graciously provided their DNA so I could utilize it to figure how who matched whom.  Like a huge family puzzle, with no picture on the box cover.

nav 23andme 10

On down the list a ways are folks who I match but with whom I’m not yet sharing.  Geeze, guess I’d better try to fix that!

nav 23andme 11

Looking down the list, I see that few have included much information, which is sometimes an indication that they’re either not interested or don’t know a lot about their genealogy.  But look, there’s one with quite a bit of information near the bottom of the list.  Great.  But wait….oh no….I’ve already sent an invitation and never heard back.  That’s OK though, because I can send another message by clicking on “View” and then “Compose.”  Again, I always include a personal message.  Some people include links to their family trees in these messages as well.

Searching for Surnames within Genetic Matches

Let’s say I want to be more specific and I want to target people on my match list that have a specific surname.  I want to see who among my genetic matches also shares the Bolton surname in a genealogical line.

In the “search matches” box at the top of the list of names, I entered Bolton, my father’s mother’s maiden name.

The list returned is small.  The first person, Stacy, is my cousin and I know her genealogy quite well, so that surname match is expected.  But I don’t’ know the second person, Janet, and I need to investigate this further.

nav 23andme 12

Remember, this is a surname search of those who match genetically.  Even though Janet and I share a common surname and some DNA, our match may NOT be through the Bolton line.  In fact, it could be on my mother’s side instead.

So as a quick check, since I manage my Cousin Stacy’s DNA account, and she is related through my father, I’m going to see if she matches Janet too. If so, then that means the match is from my father’s line, and could well be the Bolton family.  This technique is called triangulation.

Stacy does not match Janet, so that means that more genealogy work is in order to see if the Henry Bolton (1759-1846) ancestral line is our common line. It could simply be that Stacy and Janet are too far removed from a common ancestor and Bolton is the correct genealogy line, but they don’t share a large enough segment of DNA to show up on each other’s lists.

The other potential issue is that either Stacy or Janet is over their 1000 match limit imposed by 23andMe, so they might actually match each other, but have fallen off the match list.  This is becoming a larger and larger issue.  I’m over that limit as are most people who have Jewish heritage and many who carry colonial American genealogy.  So far, 23andMe has declined to address this growing issue.  It makes drawing any conclusions from this type of triangulation impossible through a vendor-imposed handicap.

Composite Surnames

On the DNA Relatives Page, click on the surname link in the upper right hand corner.  What this shows you are the number of the various surnames on your list as compared to how rare they are in the general population.  This is your signal that something is up, so to speak, and it might be your lucky day.

My most “enriched” surname is Vannoy.  This means that it appears 7 times in my match list, including as one of my own historical surnames, and it’s quite rare otherwise, which is why the 98 on the enrichment bar and the fact that is it is my more prevalent rare surname.

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Looking down the list, this implies that maybe Henley is one of my family names that I’m not aware of.  Maybe I should contact the Henley matches and see if there is anything in common between them, genealogically, and if I have any dead ends where their ancestors are located.  Maybe I should see if their DNA and mine overlaps in any common location.  The easiest way to do that would be to use the downloaded spreadsheet via www.dnagedcom.com because then we can see everyone who matches those segments of DNA, including those who have tested at Family Tree DNA because I’ve downloaded that file into my spreadsheet as well.

You can click on the surname and your matches will be displayed, including ones you’re sharing with and ones you aren’t.  In this case, I clicked on McNeil and discovered my matches are all my cousins, so nothing new to be discovered here.

I did notice that not all my surnames are present.  For example, Estes is missing.  I’m not sure how 23andMe selects the names to include, and there is no “page help,” so I’m just glad for the ones that are present on the list.

Chromosome Comparison Tool

Ok, now that you’ve found matches and they are sharing with you, what’s next?  The next tool is the chromosome comparison tool, found under Family and Friends, then Family Traits.

This tool allows you to compare any two people on your list of matches, including the X chromosome which is inherited differently and can be a very important genealogy hint.

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Here’s  a comparison of me and my cousin, Cheryl.  Her father and my grandfather were brothers, so we share quite a bit of DNA.  And because I know where it comes from, genealogically, anyone who matches both of us on these segments shares our ancestry too.  No, you can’t do that “compare all” function at 23andMe, but your downloaded spreadsheet will handle that quite nicely.

Update:  Venice points out that Family Traits does one thing that Family Inheritance: Advanced doesn’t do – it identifies fully identical segments vs. half identical segments.  Most segments between genetic relatives are half identical, but (full) siblings will have a fair amount that’s fully identical.  Family Traits also shows the locations of the centromeres and other low-data zones.

Family Inheritance, Advanced

Under the Ancestry Tools tab, there is one more tool I want to discuss briefly.  Unfortunately, it’s not as useful as it could be because of the way it has been implemented.

This tool allows you to compare yourself with up to three other kits whom you match, except for public matches.  Unfortunately, I have several public matches and I’d love to be able to do this comparison.  For example, I’d like to compare myself to my cousin Stacy and Janet, but because Janet is a public match, she’s not available on my list:(

Update:  Kitty has found a way to allow for Public match comparisons.  “To offer to share with a public person you have to click on their name at the left to go to their profile and then click the words Invite (name) to share genomes located at the top right.”  Thank you Kitty!

Red Herring Matches

Let’s use Family Inheritance Advanced as an example of two people who match me on the same segment, but are from opposite sides of my family.  I know when we talk about this, people secretly say to themselves, “yea, but how often does that really happen, I mean, what are the chances.?”  Well, here’s the answer.  Better chances that winning the lottery, for sure, and I mean the scratch off tickets where you win a dollar!

My cousins Stacy and Cheryl are from Dad’s and Mom’s side of the family, respectively.  We know they don’t share common ancestry, but look, they both match me on four of the same segments.

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How is this possible, you ask.  Remember, I have two halves of each chromosome, one from Mom and one from Dad.  It just so happens that Cheryl and Stacy both match me on the same segment, but they are actually matching two different sides of my chromosome.

Now let’s prove this to the doubting Thomas’s out there.

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Here is the comparison of Cheryl and Stacy directly to each other.  They do have one small matching segment, 6 cM, so on the small side.  But they don’t match each other on any of the segments where I match both of them.

If they did match each other and me on the same locations, it would mean that we three have common ancestry.  This is another example of triangulation.

The fact that they match each other on one segment could also mean they have distant common ancestry, which could be from one of our common lines or a line that I don’t share with them, or it could mean they have an identical by state (IBS) segment, meaning they come from a common population someplace hundreds to thousands of years ago.

The real message here is that you can never, ever, assume.  We all know about assume, and if you do, it will.  In this case, assuming would have been easy if you didn’t have the big picture, because both of these family lines contain Millers from Ohio living in close proximity in the 1800s.  However these Miller lines have been proven not to be the same lines (via Yline testing) and therefore, any assumptions would have been incorrect, despite the suggestive location and in-common names. Furthermore, one Miller line married into my cousin Stacy’s line after our common ancestor, so is not blood related to me.  But conclusions are easy to jump to, especially for excited or inexperienced genetic genealogists.  It’s tempting even for those of us who are fairly seasoned now, but after you’ve been burned a few times, you do learn some modicum of restraint!

Downloading Your Raw Data

Downloading your raw data is not the same thing as using www.dnagedcom.com to download your chromosome start and stop locations for your matches.  Your raw data is just that, raw data.

It looks like this and it’s thousands and thousands of lines long. It’s your actual values at different DNA locations.  The rsid is the location on the reference human genome, followed by the chromosome number, the position address on that chromosome, and the nucleotide given to you by each of your parents.

# rsid  chromosome position    genotype

rs3094315    1        742429         AA

It’s doesn’t mean anything in this format, but after analyzing it using complex software, this information, combined, can tell you who you match, your ethnicity and more, of course.  You’ll want to do a couple of things with your raw data file.

First, use this link to download it.  They’ve hidden the link well on their site.  I can never find it, so I just keep this link handy.

https://www.23andme.com/you/download/

Consider uploading your raw data to www.gedmatch.com.  It’s a donation site (meaning free but donations accepted) created for genetic genealogists by genetic genealogists and it has a lot more tools than any of the testing companies alone.  Think of it as a genetic genealogy sandbox.  One of the benefits is that people from all 3 testing companies, 23andMe, Family Tree DNA and Ancestry.com can upload their data and compare to each other.  The down side is that many people don’t know about GedMatch and don’t utilize it.

Last, consider transferring your results to Family Tree DNA.  At Family Tree DNA, the people who test are interested in genealogy – they are genealogists or their family members.  You are much more likely to receive responses to inquiries and you don’t have to invite people and wait for acceptance.  Even when people don’t reply to your inquiries at Family Tree DNA, you can still utilize the comparison tools to compare up to any 5 of matches, seeing where they match you and each other.  I’ve utilized this tool numerous times, an example of which you can find in the Davenport article and the Autosomal Basics article.  To transfer your results to Family Tree DNA for $99, which is less than retesting, click on this link, then click on “Products.”

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Then scroll down to “Third Party” and the product you’re looking for is “Transfer Relative Finder” which used to be the name of the 23andMe products before they rearranged the furniture.nav 23andme 18

Happy swimming in the genetic genealogy pools. Let’s hope you meet some family there!