Mitochondrial DNA Results from the Big Y Test

Say what? Mitochondrial results from a Y DNA test? You must be kidding? It’s April Fool’s Day, right???

“Not funny,” you say…

Keep reading:)

Felix’s Thought Logs, by Felix Chandrakumar, a software engineer from Australia, ran a nice article about the deliverable report from a company called YFull that does an analysis of the output of the fully sequenced Y chromosome files from either Family Tree DNA (Big Y) or Full Genomes (Full Y). I did find this report very interesting, but having said this, I would NOT go so far as to recommend this service. It’s free, and I know that’s enticing, but there really is no such thing as a free lunch.

YFull lists no terms of service. What are they doing with the DNA results, other than analyzing them for you? Are they also processing or retaining them in some other manner, for something else? There has to be a benefit of some sort to YFull, and they don’t tell us what that is. You can read more about YFull here. The YFull service is located in Moscow, Russia.

Until I fully understand what is being done with the files and results, I certainly will never recommend anyone send files to an unknown foreign entity under uncertain circumstances. Furthermore, Russia is outside the legal reach of people in the US if a dispute arises. There is no available recourse. Looking at the owners, and the websites they are involved with, are the DNA results being incorporated into those sites? Again, without terms of service and full disclosure, as consumers, we have no way of knowing.

Now that we have that housekeeping out of the way, let’s take a look at a very unusual report.

When reviewing Felix’s YFull results, I was very surprised to notice one screen in particular – his mitochondrial DNA.

Felix mito

This, of course, begs the question of how, on a Y chromosome test, can one obtain mitochondrial DNA results? To the best of my knowledge, there is no mitochondria on the Y chromosome.

mito y nucleus

In fact, the mitochondrial isn’t even in the cell nucleus with the X and Y chromosomes – it’s outside. So, how can the Y test be returning mitochondrial results?

I turned to Dr. David Mittelman, PhD, geneticist and Chief Scientific Officer for Gene by Gene, parent company of Family Tree DNA for answers.

Dr. Mittelman has been gracious enough to provide insights into how this happens.  See, no April Fools joke afterall!

Q. Dr. Mittelman, can you please confirm that the mitochondrial DNA and the Y chromosome are completely separate entities?

A. The mtDNA and Y chromosome are still separate entities :)

Q. Then how are mitochondrial DNA results being returned in conjunction with the Big Y test?

A. When you perform capture sequencing, you enrich for specific targets (in this case, the Y chromosome) but enrichment means you also get trace amounts of other sequences in the genome.

Q. Are these mitochondrial results high quality? Does the Big Y test cover all 16,569 mitochondrial DNA locations, like the full mitochondrial sequence test?

A.These mitochondrial results do not represent a high quality, high coverage sequence; and it does not give you the full mtDNA sequence — however in many cases you get enough markers to assign a haplogroup. You would probably prefer the complete sequence, however, if you want to use mtDNA for genealogical matching. Furthermore, since these are incidental findings, they are not reported on your mitochondrial page at Family Tree DNA, so no matching is possible. Only the specific mitochondrial tests designed for complete mitochondrial DNA coverage are reported on your personal page as results.

Q. If there are mitochondrial insertions, deletions or heteroplasmies, will the Big Y test be able to “see” those?

A. Yes but again the biggest limitation is coverage. At lower coverage and with fewer high quality reads, it is harder to resolve heteroplasmies and even some insertions and deletions. The BigY does not contain enough information to fully characterize all your variants in your mtDNA sequence, which is why we do not advertise it as such. It is exciting, however, to see that others are trying to extract value from the data. That is a key reason we make the raw data available. We are eager to see what complementary tools and insights other folks come up with.

Q. So, from what you’re saying, it sounds like the Big Y sequencing process may return an indeterminate amount of mitochondrial information, but it should not be relied upon as there is no guarantee that it is accurate or complete. In other words, they are simply incidental findings that are included coincidentally. Haplogroups predicted from this information may be incorrect or incomplete based on the quality or lack thereof of the incidental mtDNA data.

A. Certainly we did not design BigY to return your mtDNA sequence and I have not personally reviewed the accuracy of YFull, but it is possible for some customers to get some bonus mtDNA data. I think to gain more clarity it would be valuable to compare mtDNA data from the BigY to high quality, full mtDNA sequence from the same customers. Comparing that data would tell us more about the accuracy and value.

Following up on Dr. Mittelman’s suggestion, I checked with Felix about the accuracy of his mitochondrial results.

Felix has had his full mitochondrial sequence tested at Family Tree DNA. He reported that the YFull report found all of his 31 mutations, except for one in the coding region, and that another mutation, 315.1 was reported as 310. His haplogroup is accurate, but if some of the mutations missed were haplogroup defining mutations, it certainly could be, and probably would be estimated incorrectly. Not at all bad though, for an incidental freebie!

I want to thank Felix for being gracious enough to allow me to use his mtDNA results and Dr. Mittelman for his insights.

 

March Madness mtDNA Mega Weekend Sale

mtDNA rope

Family Tree DNA has blown the doors off the pricing of mitochondrial DNA full sequence testing this time – but just for a limited time. This is only a weekend sale and it ends April 1.

To put this in perspective, when I purchased the full sequence test, a few years ago, the price of the test was just south of a grand. Today, if you order the full sequence test, it’s only $139, reduced from $199. There’s no need anymore to consider testing at the lower levels. The only reason to have ever tested at lower levels was price – and now that’s not a consideration anymore.

If you have already tested at the HVR1 or HVR2 levels, there are sales on upgrades to the MEGA, or full sequence test.

  • mtHVR1toMEGA Upgrade – Was $149 US Now $99 US
  • mtHVR2toMEGA Upgrade – Was $159 US Now $89 US

Your mitochondrial DNA will track your direct matrilineal line – meaning that of your mother, her mother, her mother right on up your family tree – like a laser light beam – back beyond surnames into the mists of history. Your mitochondrial line is shown by the red circles, below. Everyone, males and females, carry mitochondrial DNA – so everyone can take this test.

Y and mito

Who were your people? Where were they from? What can we tell about them and their migration and settlement patterns and history? Those secrets are all held in your mitochondrial DNA, passed from an entire series of female ancestors directly to you.

To not test your mitochondrial DNA is to not open the door of discovery readily available to you!  And who among genealogists doesn’t want to know about their ancestors?  Most of us want to know every scrap available, and mitochondrial DNA is a very big piece of your own personal family history, compliments of your maternal ancestors!

I’ve written several articles on my blog about mitochondrial DNA in different contexts.

http://dna-explained.com/?s=mitochondrial

One of my favorite, though, is about my own journey of mitochondrial discovery.

CeCe Moore also wrote an article today about mitochondrial DNA testing.

But you’ll have to hurry to get this price. The sale ends on April 1, at 11:59 PM, Central Time – and that’s no April Fool joke! Click here to order a new test or sign on to your personal page and click on “upgrade” if you have already tested at the HVR1 or HVR2 levels.

Haplogroup Comparisons Between Family Tree DNA and 23andMe

Recently, I’ve received a number of questions about comparing people and haplogroups between 23andMe and Family Tree DNA.  I can tell by the questions that a significant amount of confusion exists about the two, so I’d like to talk about both.  In you need a review of “What is a Haplogroup?”, click here.

Haplogroup information and comparisons between Family Tree DNA information and that at 23andMe is not apples and apples.  In essence, the haplogroups are not calculated in the same way, and the data at Family Tree DNA is much more extensive.  Understanding the differences is key to comparing and understanding results. Unfortunately, I think a lot of misinterpretation is happening due to misunderstanding of the essential elements of what each company offers, and what it means.

There are two basic kinds of tests to establish haplogroups, and a third way to estimate.

Let’s talk about mitochondrial DNA first.

Mitochondrial DNA

You have a very large jar of jellybeans.  This jar is your mitochondrial DNA.

jellybeans

In your jar, there are 16,569 mitochondrial DNA locations, or jellybeans, more or less.  Sometimes the jelly bean counter slips up and adds an extra jellybean when filling the jar, called an insertion, and sometimes they omit one, called a deletion.

Your jellybeans come in 4 colors/flavors, coincidentally, the same colors as the 4 DNA nucleotides that make up our double helix segments.  T for tangerine, A for apricot, C for chocolate and G for grape.

Each of the 16,569 jellybeans has its own location in the jar.  So, in the position of address 1, an apricot jellybean is always found there.  If the jellybean jar filler makes a mistake, and puts a grape jellybean there instead, that is called a mutation.  Mistakes do happen – and so do mutations.  In fact, we count on them.  Without mutations, genetic genealogy would be impossible because we would all be exactly the same.

When you purchase a mitochondrial DNA test from Family Tree DNA, you have in the past been able to purchase one of three mitochondrial testing levels.  Today, on the website, I see only the full sequence test for $199, which is a great value.

However, regardless of whether you purchase the full mitochondrial sequence test today, which tests all of your 16,569 locations, or the earlier HVR1 or HVR1+HVR2 tests, which tested a subset of about 10% of those locations called the HyperVariable Region, Family Tree DNA looks at each individual location and sees what kind of a jellybean is lodged there.  In position 1, if they find the normal apricot jellybean, they move on to position 2.  If they find any other kind of jellybean in position 1, other than apricot, which is supposed to be there, they record it as a mutation and record whether the mutation is a T,C or G.  So, Family Tree DNA reads every one of your mitochondrial DNA addresses individually.

Because they do read them individually, they can also discover insertions, where extra DNA is inserted, deletions, where some DNA dropped out of line, and an unusual conditions called a heteroplasmy which is a mutation in process where you carry some of two kinds of jellybean in that location – kind of a half and half 2 flavor jellybean.  We’ll talk about heteroplasmic mutations another time.

So, at Family Tree DNA, the results you see are actually what you carry at each of your individual 16,569 mitochondrial addresses.  Your results, an example shown below, are the mutations that were found.  “Normal” is not shown.  The letter following the location number, 16069T, for example, is the mutation found in that location.  In this case, normal is C.  In the RSRS model of showing mitochondrial DNA mutations, this location/mutation combination would be written as C16069T so that you can immediately see what is normal and then the mutated state.  You can click on the images to enlarge.

ftdna mito results

Family Tree DNA gives you the option to see your results either in the traditional CRS (Cambridge Reference Sequence) model, above, or the more current Reconstructed Sapiens Reference Sequence (RSRS) model.  I am showing the CRS version because that is the version utilized by 23andMe and I want to compare apples and apples.  You can read about the difference between the two versions here.

Defining Haplogroups

Haplogroups are defined by specific mutations at certain addresses.

For example, the following mutations, cumulatively, define haplogroup J1c2f.  Each branch is defined by its own mutation(s).

Haplogroup Required Mutations  
J C295T, T489C, A10398G!,   A12612G, G13708A, C16069T
J1 C462T, G3010A
J1c G185A, G228A,   T14798C
J1c2 A188G
J1c2f G9055A

You can see, below, that these results, shown above, do carry these mutations, which is how this individual was assigned to haplogroup J1c2f. You can read about how haplogroups are defined here.

ftdna J1c2f mutations

At 23andMe, they use chip based technology that scans only specifically programmed locations for specific values.  So, they would look at only the locations that would be haplogroup producing, and only those locations.  Better yet if there is one location that is utilized in haplogroup J1c2f that is predictive of ONLY J1c2f, they would select and use that location.

This same individual at 23andMe is classified as haplogroup J1c2, not J1c2f.  This could be a function of two things.  First, the probes might not cover that final location, 9055, and second, 23andMe may not be utilizing the same version of the mitochondrial haplotree as Family Tree DNA.

By clicking on the 23andMe option for “Ancestry Tools,” then “Haplogroup Tree Mutation Mapper,” you can see which mutations were tested with the probes to determine a haplogroup assignment.  23andMe information for this haplogroup is shown below.  This is not personal information, meaning it is not specific to you, except that you know you have mutations at these locations based on the fact that they have assigned you to the specific haplogroup defined by these mutations.  What 23andMe is showing in their chart is the ancestral value, which is the value you DON’T have.  So your jelly bean is not chocolate at location 295, it’s tangerine, apricot or grape.

Notice that 23andMe does not test for J1c2f.  In addition, 23andMe cannot pick up on insertions, deletions or heteroplasmies.  Normally, since they aren’t reading each one of your locations and providing you with that report, missing insertions and deletions doesn’t affect anything, BUT, if a deletion or insertion is haplogroup defining, they will miss this call.  Haplogroup K comes to mind.

J defining mutations

J1 defining mutations

J1c defining mutations

23andMe never looks at any locations in the jelly bean jar other than the ones to assign a haplogroup, in this case,17 locations.  Family Tree DNA reads every jelly bean in the jelly bean jar, all 16,569.  Different technology, different results.  You also receive your haplogroup at 23andMe as part of a $99 package, but of course the individual reading of your mitochondrial DNA at Family Tree DNA is more accurate.  Which is best for you depends on your personal testing goals, so long as you accurately understand the differences and therefore how to interpret results.  A haplogroup match does not mean you’re a genealogy match.  More than one person has told me that they are haplogroup J1c, for example, at Family Tree DNA and they match someone at 23andMe on the same haplogroup, so they KNOW they have a common ancestor in the past few generations.  That’s an incorrect interpretation.  Let’s take a look at why.

Matches Between the Two

23andMe provides the tester with a list of the people who match them at the haplogroup level.  Most people don’t actually find this information, because it is buried on the “My Results,” then “Maternal Line” page, then scrolling down until your haplogroup is displayed on the right hand side with a box around it.

Those who do find this are confused because they interpret this to mean they are a match, as in a genealogical match, like at Family Tree DNA, or like when you match someone at either company autosomally.  This is NOT the case.

For example, other than known family members, this individual matches two other people classified as haplogroup J1c2.  How close of a match is this really?  How long ago do they share a common ancestor?

Taking a look at Doron Behar’s paper, “A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root,” in the supplemental material we find that haplogroup J1c2 was born about 9762 years ago with a variance of plus or minus about 2010 years, so sometime between 7,752 and 11,772 years ago.  This means that these people are related sometime in the past, roughly, 10,000 years – maybe as little as 7000 years ago.  This is absolutely NOT the same as matching your individual 16,569 markers at Family Tree DNA.  Haplogroup matching only means you share a common ancestor many thousands of years ago.

For people who match each other on their individual mitochondrial DNA location markers, their haplotype, Family Tree DNA provides the following information in their FAQ:

    • Matching on HVR1 means that you have a 50% chance of sharing a common maternal ancestor within the last fifty-two generations. That is about 1,300 years.
    • Matching on HVR1 and HVR2 means that you have a 50% chance of sharing a common maternal ancestor within the last twenty-eight generations. That is about 700 years.
    • Matching exactly on the Mitochondrial DNA Full Sequence test brings your matches into more recent times. It means that you have a 50% chance of sharing a common maternal ancestor within the last 5 generations. That is about 125 years.

I actually think these numbers are a bit generous, especially on the full sequence.  We all know that obtaining mitochondrial DNA matches that we can trace are more difficult than with the Y chromosome matches.  Of course, the surname changing in mitochondrial lines every generation doesn’t help one bit and often causes us to “lose” maternal lines before we “lose” paternal lines.

Autosomal and Haplogroups, Together

As long as we’re mythbusting here – I want to make one other point.  I have heard people say, more than once, that an autosomal match isn’t valid “because the haplogroups don’t match.”  Of course, this tells me immediately that someone doesn’t understand either autosomal matching, which covers all of your ancestral lines, or haplogroups, which cover ONLY either your matrilineal, meaning mitochondrial, or patrilineal, meaning Y DNA, line.  Now, if you match autosomally AND share a common haplogroup as well, at 23andMe, that might be a hint of where to look for a common ancestor.  But it’s only a hint.

At Family Tree DNA, it’s more than a hint.  You can tell for sure by selecting the “Advanced Matching” option under Y-DNA, mtDNA or Family Finder and selecting the options for both Family Finder (autosomal) and the other type of DNA you are inquiring about.  The results of this query tell you if your markers for both of these tests (or whatever tests are selected) match with any individuals on your match list.

Advanced match options

Hint – for mitochondrial DNA, I never select “full sequence” or “all mtDNA” because I don’t want to miss someone who has only tested at the HVR1 level and also matches me autosomally.  I tend to try several combinations to make sure I cover every possibility, especially given that you may match someone at the full sequence level, which allows for mutations, that you don’t match at the HVR1 level.  Same situation for Y DNA as well.  Also note that you need to answer “yes” to “Show only people I match on all selected tests.”

Y-DNA at 23andMe

Y-DNA works pretty much the same at 23andMe as mitochondrial meaning they probe certain haplogroup-defining locations.  They do utilize a different Y tree than Family Tree DNA, so the haplogroup names may be somewhat different, but will still be in the same base haplogroup.  Like mitochondrial DNA, by utilizing the haplogroup mapper, you can see which probes are utilized to determine the haplogroup.  The normal SNP name is given directly after the rs number.  The rs number is the address of the DNA on the chromosome.  Y mutations are a bit different than the display for mitochondrial DNA.  While mitochondrial DNA at 23andMe shows you only the normal value, for Y DNA, they show you both the normal, or ancestral, value and the derived, or current, value as well.  So at SNP P44, grape is normal and you have apricot if you’ve been assigned to haplogroup C3.

C3 defining mutations

As we are all aware, many new haplogroups have been defined in the past several months, and continue to be discovered via the results of the Big Y and Full Y test results which are being returned on a daily basis.  Because 23andMe does not have the ability to change their probes without burning an entirely new chip, updates will not happen often.  In fact, their new V4 chip just introduced in December actually reduced the number of probes from 967,000 to 602,000, although CeCe Moore reported that the number of mtDNA and Y probes increased.

By way of comparison, the ISOGG tree is shown below.  Very recently C3 was renamed to C2, which isn’t really the point here.  You can see just how many haplogroups really exist below C3/C2 defined by SNP M217.  And if you think this is a lot, you should see haplogroup R – it goes on for days and days!

ISOGG C3-C2 cropped

How long ago do you share a common ancestor with that other person at 23andMe who is also assigned to haplogroup C3?  Well, we don’t have a handy dandy reference chart for Y DNA like we do for mitochondrial – partly because it’s a constantly moving target, but haplogroup C3 is about 12,000 years old, plus or minus about 5,000 years, and is found on both sides of the Bering Strait.  It is found in indigenous Native American populations along with Siberians and in some frequency, throughout all of Asia and in low frequencies, into Europe.

How do you find out more about your haplogroup, or if you really do match that other person who is C3?  Test at Family Tree DNA.  23andMe is not in the business of testing individual markers.  Their business focus is autosomal DNA and it’s various applications, medical and genealogical, and that’s it.

Y-DNA at Family Tree DNA

At Family Tree DNA, you can test STR markers at 12, 25, 37, 67 and 111 marker levels.  Most people, today, begin with either 37 or 67 markers.

Of course, you receive your results in several ways at Family Tree DNA, Haplogroup Origins, Ancestral Origins, Matches Maps and Migration Maps, but what most people are most interested in are the individual matches to other people.  These STR markers are great for genealogical matching.  You can read about the difference between STR and SNP markers here.

When you take the Y test, Family Tree DNA also provides you with an estimated haplogroup.  That estimate has proven to be very accurate over the years.  They only estimate your haplogroup if you have a proven match to someone who has been SNP tested. Of course it’s not a deep haplogroup – in haplogroup R1b it will be something like R1b1a2.  So, while it’s not deep, it’s free and it’s accurate.  If they can’t predict your haplogroup using that criteria, they will test you for free.  It’s called their SNP assurance program and it has been in place for many years.  This is normally only necessary for unusual DNA, but, as a project administrator, I still see backbone tests being performed from time to time.

If you want to purchase SNP tests, in various formats, you can confirm your haplogroup and order deeper testing.

You can order individual SNP markers for about $39 each and do selective testing.  On the screen below you can see the SNPs available to purchase for haplogroup C3 a la carte.

FTDNA C3 SNPs

You can order the Geno 2.0 test for $199 and obtain a large number of SNPs tested, over 12,000, for the all-inclusive price.  New SNPs discovered since the release of their chip in July of 2012 won’t be included either, but you can then order those a la carte if you wish.

Or you can go all out and order the new Big Y for $695 where all of your Y jellybeans, all 13.5 million of them in your Y DNA jar are individually looked at and evaluated.  People who choose this new test are compared against a data base of more than 36,000 known SNPs and each person receives a list of “novel variants” which means individual SNPs never before discovered and not documented in the SNP data base of 36,000.

Don’t know which path to take?  I would suggest that you talk to the haplogroup project administrator for the haplogroup you fall into.  Need to know how to determine which project to join, and how to join? Click here.  Haplogroup project administrators are generally very knowledgeable and helpful.  Many of them are spearheading research into their haplogroup of interest and their knowledge of that haplogroup exceeds that of anyone else.  Of course you can also contact Family Tree DNA and ask for assistance, you can purchase a Quick Consult from me, and you can read this article about comparing your options.

Houston Chronicle Article Features Gene by Gene Founders

On Sunday, March 16th, 2014, the Houston Chronicle features an article about Houston’s own entrepreneurs, Max Blankfeld and Bennett Greenspan who founded Gene by Gene, parent company of Family Tree DNA.  Below, in a photo from the Chronicle, they hold samples of DNA trayed and ready to run in their Gene by Gene lab.

Max and Bennett

How many of you know that the pair began as a photographic film salesman and a watchmaker?  This just proves what passion and innovation can and will do.  Impossible is not a word either man knows.

Begun in 2000 as a retirement business, today Family Tree DNA has tested over 600,000 people directly and another half a million people through National Geographic through the Genographic and Geno 2.0 projects.

Their business model: Buy what you can afford. Don’t hire anyone you might have to lay off. Invest in automation and technology.

This seems to be working, as they are profitable and have provided a total of over 5 million discrete tests, between Family Tree DNA and the other Gene by Gene testing companies which provide medical and paternity testing.

The story of how the company began is legendary in DNA circles.  Bennett Greenspan, a frustrated genealogist who had hit a dead end approached Dr. Michael Hammer at the University of Arizona.  One might suggest that approached isn’t really the correct word.  Hounded might be better.  Bennett understood that his Y chromosome would match that of someone else who shared a paternal ancestor, and he wanted to find a lab to do that test.  Michael Hammer finally simply acquiesced to get rid of Bennett, with the now infamous throw away line, “You know, someone should start a business doing this.”  Never, never say that to an entrepreneur.

As reported in the Chronicle, reflectively, Dr. Hammer, an adviser to Gene by Gene and a regular speaker at the Family Tree DNA annual genetics conference, says today, “It was just the right time, right place. No one thought this was going to turn into anything.”  Michael had obviously never met a man like Bennett.

I’ve known Bennett for 13 or 14 years now.  It’s easy to see him as a successful businessman.  But to know Bennett is to remember that he is truly a genealogist at heart, and everything he does with Family Tree DNA has genealogy as its heart and soul.  If you walk into his office, you will be immediately reminded of this fact, and it’s hard to see Bennett as anything else other than one of us – just a kind-hearted genealogist seeking answers.  In the photo below from the Chronicle, Bennett stands in front of his ancestor timeline which resides on his office wall.  I wonder how many of these ancestors he has represented by DNA haplogroups today.

Bennett in office

Thank you so much Bennett, for pushing that envelope, hounding Dr. Hammer and birthing genetic genealogy.  Today, Max and Bennett are truly shepherding consumer genetics to the next step.

“We took science that was performed in a stuffy lab and brought it into the general public,” Greenspan said.

Thank Heavens they did.  We are all the beneficiaries.

To read the rest of the article and for more photos, click here.

23 Ways To Be a PITA

PITANo, not PETA, the People for the Ethical Treatment of Animals, but PITA – Pain In The Arm….yes….arm…what are you thinking???

For most people, being a PITA doesn’t come naturally….so you might need some help knowing how to be one, or perhaps perfecting your PITA skills.  Yes, in case you’re wondering….my tongue is firmly implanted in my cheek.

For genetic genealogists, there are special ways to be a PITA.  Let me share some of these with you, just so you can fine tune and add to your PITA skills.

First and maybe the best ways to be a PITA, right off the bat.

1. Send e-mails with no subject or punctuation and an indecipherable topic, especially to someone you’ve never communicated with before.  Here’s an example.  You can just copy and paste this and send it to anyone you want to irritate or confuse.

“i would love to have any information you could give me…..thanks…..”

I so want to send this person something about penile implants.  Is this wrong?

2. Send e-mails with no capitals or punctuations.  This is always a wonderful way to impress people.

i just wanted to let you know that i have no idea how to type or how to use the period or comma keys or how to use the shift button i’m also using the fact that i’m using my phone as an excuse not to use punctuation however I can manage to type half of my life story for you to try to decipher so get out your special decoder ring

3. BETTER YET, SEND THE ENTIRE MESSAGE, INCLUDING SEVERAL PAGES OF YOUR ANCESTORS NAMES WITH NO DATES OR OTHER IDENTIFYING INFORMATION IN ALL CAPITALS.  THEN ASK FOR ANY INFORMATION THAT PERSON MIGHT HAVE ABOUT THOSE ANCESTORS.  THIS IS ESPECIALLY USEFUL WHEN FIRST INTRODUCING YOURSELF AND LETS YOUR NEW CONTACT KNOW JUST HOW IMPORTANT THEY ARE AND HOW MUCH FUN IT’S GOING TO BE TO COMMUNICATE WITH YOU.

4. When a match asks you for genealogy information, just send them a link to your Ancestry.com tree.  You can then sit back and laugh, knowing that they have no idea where to search in your 35,723 people for a common ancestor without looking for every surname they have.  Plus, you have the added benefit that Ancestry will help you be a PITA by attaching your tree to their account like a giant kudzu vine that they can’t disentangle without knowing the secret handshake.

5. When a match asks you for genealogy information, never, ever send them something actually useful, like a pedigree chart with an index.  Instead send them rambling e-mails with disconnected tidbits from both sides of your family, or that link to your Ancestry tree.  Go to sleep then, knowing they will be up all night trying to figure this out.

6. Ask for, or better yet, demand free consulting.  Select someone at random (not me please, I already receive more than my share – 17 yesterday alone) and send them a rambling stream-of-consciousness e-mail several pages long.  At the end, tell them that you can’t afford to pay anything, but ask if they would tell you “what they think.”  Before sending these to anyone in the genetic genealogy community, send several to other professionals, physicians or lawyers in your community and see how that works out?

Now, if someone is a project volunteer, that’s a bit different.  They still don’t “owe” you free consulting, but they have set themselves forth as a volunteer resource.  Still, try to be respectful of their time and be brief and concise in your requests.

In other words, the 21 page e-mail I received this week from Person Unknown demanding that I, as a project administrator, figure out how the “requester” was related to three people in the large Cumberland Gap project (also persons unknown) was, well, ahem, a bit over the top, to put it mildly.  No, I confess, I did not read all 21 pages and the only reason I know it WAS 21 pages long is because I wanted to use it as a bad example.  If that was your e-mail and I’ve just offended you, well, I’m sorry you’re offended, but that is not the way to win friends and influence people, nor to get your questions answers or your problems solved.  It is, however, a great way to be a PITA.  In fact, you win this week’s PITA award!

Here’s an example of a reasonable, concise question from my blog:

“Thanks for that explanation, I needed that information. Still would like to know what a “back mutation” is.”

And the answer:

“A back mutation is when a mutations happens, like from A to C, and then the reverse happens, a mutation from C to A. It initially looks like no mutation happened, unless you are aware of the intermediate step and that two mutations actually happened.”

There’s a big difference between a simple one or two line general DNA question and a multi-page personal epistle that the receiver has to read three times and make charts to even begin to unravel or understand, so, to be a PITA – always make yourself annoying and then you can wonder why you never receive replies from people.  Then complain about not receiving replies.

Oh, and if you do write to a project administrator, never, ever tell them how or why you are writing specifically to them – it’s much more fun to leave them guessing.  The sender of the 21 page epistle did not SAY it was the Cumberland Gap project – they left that for me to decipher.

7. Skim articles, don’t click on the links, and then ask questions of the author that would have been answered if you had clicked on the links they provided in the first place.  They love receiving several of these e-mails every day!

Now, if you have DNA tested at any of the three major testing companies, there special ways for you to be a PITA with each one.  Let me give you some fresh ideas.

At Family Tree DNA

8. Join a DNA project, any project.  Then, when the administrator sends you a welcome message, introducing themselves and asking for genealogy information, send them a nasty note.  Here’s one I received recently.  You can just use it.

“Who the hell are you and why are you contacting me.  Don’t ever contact me again.”

9. Family Tree DNA does you the very large favor of providing you with the e-mail addresses of your contacts instead of forcing you to go through a message system like at 23andMe and Ancestry.

When sending an e-mail to someone you match, be sure to never include the name of the person you match, or what kind of a test you took that matches.  This will confuse them and make them really want to answer your inquiry.  Many people manage test kits for several people and if you don’t put the name of the person you match in your e-mail, they will probably think it’s their kit, and then they will either spend a lot of time looking for matches and/or putting together genealogy info to send to you that is not useful.  Then, after you receive the info, tell them you’re sorry, but the match was to a different person.  That will truly endear you to them.

10. Don’t ever update your e-mail address…then complain online and loudly about how you never receive contacts from either your project administrator or your contacts/matches.

11. Don’t upload your GEDCOM file either, because someone might accidentally discover a common surname match or a common ancestor, and that would be just awful.  It would also provide Family Tree DNA with the information to bold matching surnames on your autosomal match list for you, AND you’d get a $10 coupon…all of which would be just terrible.

12. Volunteer to be a project administrator, then do nothing at all.  Leave your project entirely ungrouped, and refuse any assistance.  In this case, you really don’t have to DO anything to be a PITA.

Better yet, create an off-site (non-FTDNA) website instead of using the one at Family Tree DNA and remove any information that could be useful to someone searching for their ancestral line.  Here’s an example.

Private project no useful info

Don’t want to create your own website?  Well, you can be almost as large a PITA by using the Family Tree DNA page and simply disabling anything useful, like, you know, most distant ancestor.  That way people can see that there is a project and their line MIGHT be hidden in there, but they have no way to find out other than contacting you.  Then, don’t answer, of course.

ftdna project no names

At 23andMe

13. Give yourself a really innovative “screen name,” like, say “Your cousin” or “3rd cousin” or better yet, “My Mother.”  That way when you send contact requests or sharing requests to people, it looks like it is coming from their mother…and if their mother has already passed over…well…let’s just say your contact request could be really startling.  Worse yet, if that person matches two people who are equally as creative and both named themselves “My Mother,” how will they ever tell you apart???  And can you really have two mothers?  OMG, I feel an identity crisis coming on…

14. Tell your contact that you are really interested in genealogy, provide a little bit of genealogy info, just a couple tidbits, maybe a juicy morsel, but then refuse to share your DNA.

15.  Don’t provide any surname or location information.  That might give someone a clue as to how you connect – so don’t ever do that.

16.  I’d tell you to never upload your GEDCOM file, or create one, but you can actually be a larger PITA by uploading your file at 23andMe, because their file reader interface works so poorly that your match will be more frustrated trying to read the file than by not finding one at all.  So you can be a PITA whether you upload your file or not.  How’s that for good luck!

17.  Don’t ever reply to contact or sharing requests.  I know this one is already quite popular.  About 90% of the people there already do this, so you’ll be in good company.  If people at 23andMe aren’t interested in genealogy, there is an opt-out, but don’t opt out because you can be much more of a PITA by leaving yourself in the genealogy pool but never replying to anyone, especially close matches.  Drives them crazy!

At Ancestry

18. First and foremost, never, ever reply to messages.  I know that this one is very popular, because many of my DNA matches, including my closest match at Ancestry has implemented this scheme.  She, I assume, due to the name (unless I’m related to the boy named Sue) and I share a common great-grandfather.  In this case, I have photos she might really like to have.  Too bad she is being a PITA.

19. Make your tree private, AND never reply to requests.  This is the ultimate tease, because your match KNOWS the information is there, right there, hiding just out of reach, and can’t get to it.

20. Copy and paste several trees together because, after all, the names match and, hello, it wouldn’t BE on Ancestry if it wasn’t RIGHT.  Right?  You can then scare the bejesus out of someone when they discover that their non-Mormon grandfather had 7 wives and 35 kids….all while married to their grandmother.  That’s always fun.  Then, when they frantically contact you to ask about it, don’t even think about replying to that message.

21. Insist that because you and your Ancestry DNA match have a shakey leaf and a common ancestor in your tree, that you KNOW that’s your DNA match because Ancestry SAYS SO.  When your match tries to explain that connection might be incorrect, may not be your DNA match and that there is no way to prove it, at least not without utilizing tools from either GedMatch or Family Tree DNA, don’t reply to them anymore.  That will certainly solve the problem!

22.  Send random people invitations to your Ancestry tree – and be positive your tree name has absolutely no identifying words in it.  Like the one I received recently, for example, named “A Global Tree of Life.”  Yep, I can tell you right away who sent that to me and why!!!

23. Oh yes, and in true PITA-esque fashion, never, ever say “Thank you,” to anyone, ever, for anything.  Thank you is such an easy thing to say and it makes the person on the receiving end feel good about whatever it was they did for you – even if was “just” answering your question.  So don’t slip up and do this!  Otherwise, you’ll certainly be thrown out of the PITA Club!

Thank you collage

Added PITAs

24. Instead of being grateful for free things, like blogs and webpages, and simply unsubscribing or ignoring them if you don’t like them, make nasty comments.  That will certainly confirm your PITA membership and make the person providing the free content feel warm and fuzzy about the time they invest.

“How about I unsubscribe to your boring emails about your family I have been getting the last year. Ms PITA.”

 

Family Tree DNA Launches New Learning Center

Ugly light bulb

Family Tree DNA has launched a new Learning Center.  Meant to be much more comprehensive and interactive than their previous FAQs, with everything available in one centralized place, the new Learning Center encompasses a blog, the former FAQs, Webinar information including currently scheduled and archived past Webinars available,  FTDNA’s Forum, a link to group projects, Users Guides, Group Administrator Guides and tools, a glossary, links to scientific papers and more.

Learning center landing

In fact, the site is so comprehensive that there is even a tutorial about how to utilize the Learning Center.

One of the best aspects of the Learning Center is that it’s fully searchable.  Just as a test, and because I’m a skeptic, I typed the word “heteroplasmy” into the search field.  This term, if you’re not familiar, is a relatively obscure term for mitochondrial DNA.  About 2% of the people who take a full sequence test will have a heteroplasmic mutation, which is really a mutation in process where two different nucleotides are discovered at a single location.

Sure enough, there were several results presented in a drop down box and then each one has a “read more” tab and the ability for questions and comments.  OK, FTDNA, you passed the pop quiz!

learning center heteroplasmy

The Learning Center is a one stop shopping center.  You can also contact customer support through this page, or do things like look at career openings, if you’d like to live in Houston.

Family Tree DNA has made a renewed effort and commitment to stay in touch with their customer base.  I’m particularly encouraged with the “Latest News” tab.  And it’s not just because of my interview, although I was quite honored to be the first of several interviews with leaders in the genetic genealogy field published.  You can read the interview here.

Customers and project administrators have been asking for a central place to find information about products and announcements at Family Tree DNA, and it looks like the Latest News tab is going to be the new “market square” where everyone gathers to find the latest information.

Rebekah Canada, who is responsible for the Learning Center, has also been making a concerted effort to update several other lists and locations such as the genealogy-dna list at Rootsweb, the Family Tree DNA Forum and the FTDNA Facebook page with pertinent information, but it makes sense for the “go to” place linking everything together to be the Learning Center.

Best of all, you can also subscribe to new posts.  To subscribe, click on any of the “Latest News Posts” that you see on the main page.

Learning center splash page

On the right hand side of each article is a subscribe option.  This way, all the news comes directly to you – no signing on to check to see what’s new!  It’s delivered.  I love this!!!

learning center subscribe

My only negative comment…..that’s a really ugly lightbulb.  Just doesn’t seem to convey the same thing as….

bright idea cropped

Seems like the perfect opportunity for a bright idea, some creativity and a double helix design to me!

Big Y Release

Drum roll…the big day is finally here.

Family Tree DNA held a webinar meeting today to explain the new Big Y product features for a number of us who blog or otherwise educate within the genetic genealogy community.

First, the results will begin rolling today, not tomorrow.  100 will initially be released today and the balance of the initial orders will be released as they finish QA over the next month, at which point, Family Tree DNA anticipates their backlog will be resolved.  There were thousands of tests ordered.  They aren’t saying how many thousands.

First, a little background.  There are 36,562 known Y SNPs in the Family Tree DNA data base that everyone is being compared to.  In the example we saw of the delivered product, 25,749 has been found and callable at a high confidence rate in the individual being tested and were reported.  Low confidence calls are not reported on this personal delivery page, but are included in the data download files.

Big Y landing

On the customer’s personal page, there are two tabs.  The first Tab is for reporting against known SNPs.

Y page 1 cropped

The second is for Novel Variations, in other words, SNPs not on the list of 36,562 known and previously named SNPs.

Y page 2

In essence, Family Tree DNA has implemented a 4 step process.

  1. An individual’s sequenced data is compared to the SNP data base and divided into two categories, known and previously unknown.  The customer’s data is delivered based on these two categories.
  2. All customer data is being loaded into a mammoth size data base at which point it will be determined which SNPs (please see the definition of a SNP here) are actually undiscovered SNPs that will be named, and which are truly novel, family or clan variants.
  3. New SNPs that are found in enough of the population will be named and will be added to the haplotree.
  4. Novel variants will remain that, and will continue to be reported on client pages.

Family Tree DNA is still working on items 2-4.  In addition, they are working on a white paper which will be out in the next 6 weeks or so that will discuss things like the average number of novel SNPs per person being discovered, mutation rates, performance metrics and cross validation of platforms between the next gen sequencing Illumina equipment, Sanger sequencing and chip based sequencing, like the Geno 2.0 chip.

What’s Being Reported?

According to Dr. David Mittelman, the Y chromosome has about 60 million letters.  About half of those are inverted repeats and are therefore not sequenceable.

Of the balance, there are several with poor readability, for example, some that simulate the X, etc.  These are also not useful or reliable to read.

That leaves about 10 million, these being the gold standard of Y sequencing.  Family Tree DNA tries to read about 13.5 million of these base pairs.  They promised 10 million positions when they announced this product.  They are delivering between 11.5 and 12.5 million positions per person.  They also promised about 25,000 common variants, meaning known SNPs and they are delivering between 25,000 and 30,000 per person.  This is only counting medium to high confidence calls.  The low confidence calls are included in the download files, but not counted in this total or shown on your personal page.

Exactly how many locations are reported for any individual are shown on the bottom left hand side of the page.  This example is generic.  Yours might say something like, “Showing 1 of 10 of 25,000 of 36,564.”  In this case, 25,000 would be the number of SNPs read and called on your test.

Big Y total

All 25,000 or so results are being shown, both positive and negative.  That way, there is no question about whether a specific location was tested, or the outcome.  Of course, the third and fourth outcome options are a no-call or poor confidence call at that location.

All novel mutations are being reported by reference number so that they can be compared to like data from any source, as opposed to an “in-house” assigned number.

Insertions and deletions are also in the download files, but not reported on the customer’s delivery page.

Personal data is also searchable by SNP.

SNP search

Individual SNP Testing

After steps 2 and 3 have occurred, it has to be determined which SNPs are found in a high enough percentage of a population to warrant primer development to test individual SNP positions.

Family Tree DNA also clarified something from the November conference.  The 2000 SNP limit is only how many SNPs can be loaded at one time, not the total number they will ever develop primers for or test for.  They will do what makes sense in terms of the SNP being present in enough of the market to warrant primer development.  With the very large number of Novel SNPs being discovered, it wouldn’t make much sense to purchase 50 individual SNP tests at $39 each.  The break even point today, at $39, would be 17 individual SNPs, as compared to the $695 Big Y test.  I expect that eventually the demand for individual SNP testing will decrease substantially.

Downloadable Files

Available on everyone’s page is the ability to download 2 files, a VCF (variant call file) which lists the variants identified as compared to the human reference sequence and the BED file which is a text file which shows a range of positions that passed the QC.

They will also be making available the BAM raw data files within the next week or so, but are finalizing the delivery methodology due to the very large file sizes involved.

The Much Anticipated HaploTree

If I had a dollar for every time someone has asked when the new tree would be available, I’d be a rich woman.  As we all know, there have been a couple of problems with the tree.  The new tree is 7 to 8 times the size of the 2010 tree.  The tree, of course, has been cast in warm jello, an ever-moving target.  And with the SNP tsumani that has been arriving with the full sequencing of the Y chromosome, that tree will very shortly be much larger still.

Bennett Greenspan said today that an updated tree is, “Needed, desired and will be delivered.”  He went on to say that they have had two teams working together with Nat Geo for the past couple of months to both finalize the tree itself and to work on the customer interface.  Since the tree is much larger, it’s not as easy as the older trees which could be seen at a glance and easily navigated.  Furthermore, there is also the matter of integration with National Geographic.

Bennett says an updated tree will be delivered “within the next several weeks.”

New SNPs that are discerned to be SNPs and not novel/clan or family variations will then be named and added to the tree.

Integration

The initial release of Big Y data will be just that, a release of the results of the data, displayable on your personal page and downloadable.  The newly found SNPs will not initially update the current haplotree on your personal page.  This is the same issue we have today with the transfer and integration of Nat Geo data, because the tree is not current, so this is nothing new.  The implementation of the new tree however, will remedy both problems.

The Future

Never happy with what we have, genetic genealogists will want a way to match to other people on SNPs, just like we do today with STR markers.  In fact, we’ll want a way to integrate that matching and discern what it means to our own private family or clan situations.

Family Tree DNA is aware of that, planning for it, and welcomes feedback for how they can make this information even more useful in the future than it is today.

New Orders

I expect this delivery of new information via Big Y results will indeed spur a new interest in ordering this test from people who were waiting to see exactly what was being delivered.  For those people ordering now, they can expect an 8-10 week turnaround, so long as additional vials aren’t required for testing.

For More Information

Elise Friedman is holding the free Big Y Webinar tomorrow, Friday, February 28th.  You can read about it, sign up and learn how to access this and other webinars after their initial showing at this link.

Family Tree DNA FAQ pages you’ll want to visit are here and here.