STRs vs SNPs, Multiple DNA Personalities

One of the questions I receive rather regularly is about the difference between STRs and SNPs.

Generally, what people really want to understand is the difference between the products, and a basic answer is really all they want.  I explain that an STR or Short Tandem Repeat is a different kind of a mutation than a SNP or a Single Nucleotide Polymorphism.  STRs are useful genealogically, to determine to whom you match within a recent timeframe, of say, the past 500 years or so, and SNPs define haplogroups which reach much further back in time.  Furthermore SNPs are considered “once in a lifetime,” or maybe better stated, “once in the lifetime of mankind” type of events, known as a UEP, Unique Event Polymorphism, where STRs happen “all the time,” in every haplogroup.  In fact, this is why you can check for the same STR markers in every haplogroup – those markers we all know and love.

STR

This was a pretty good explanation for a long time but as sequencing technology has improved and new tests have become available, such as the Full Y and Big Y tests, new mutations are being very rapidly discovered which blurs the line between the timeframes that had been used to separate these types of tests.  In fact, now they are overlapping in time, so SNPs are, in some cases becoming genealogically useful.  This also means that these newly discovered family SNPs are relatively new, meaning they only occurred between the current generation and 1000 years ago, so we should not expect to find huge numbers of these newly developed mutations in the population.  For example, if the SNP that defined haplogroup R1b1a2, M269, occurred 15,000 years ago in one man, his descendants have had 15,000 years to procreate and pass his M269 on down the line(s), something they have done very successfully since about half of Europe is either M269 or a subclade.

Each subclade has a SNP all its own.  In fact, each subclade is defined by a specific SNP that forms its own branch of the human Y haplotree.

So far, so good.

But what does a SNP or an STR really look like, I mean, in the raw data?  How do you know that you’re seeing one or the other?

Like Baseball – 4 Bases

The smallest units of DNA are made up of 4 base nucleotides, DNA words, that are represented by the following letters:

A = Adenine
C = Cytosine
G = Guanine
T = Thymine

TACG

These nucleotides combine in pairs to form the ladder rungs of DNA, shown right that connect the helix backbones.  T typically combines with A and C usually combines with G, reaching between the backbones of the double helix to connect with their companion protein in the center.

You don’t need to remember the words or even the letters, just remember that we are looking for pattern matches of segments of DNA.

Point Mutations

Your DNA when represented on paper looks like a string of beads where there are 4 kinds of beads, each representing one of the nucleotides above.  One segment of your DNA might look like this:

Indel example 1

If this is what the standard or reference sequence for your haplotype (your personal DNA results) or your family haplogroup (ancestral clan) looks like, then a mutation would be defined as any change, addition, or deletion.  A change would be if the first A above were to change to T or G or C as in the example below:

Indel example 2

A deletion would be noticed if the leading A were simply gone.

Indel example 3

An addition of course would be if a new bead were inserted in the sequence at that location.

Indel example 4

All of the above changes involve only one location.  These are all known as Point Mutations, because they occur at one single point.

SNPs

A point mutation may or may not be a SNP.  A SNP is defined by geneticists as a point mutation that is found in more than 1% of the population.  This should tell you right away that when we say “we’ve discovered a new SNP,” we’re really mis-applying that term, because until we determine that the frequency which it is found in the population is over the 1% threshold, it really isn’t a SNP, but is still considered a point mutation or binary polymorphism.

Today, when SNPS, or point mutations are discovered, they are considered “private mutations” or “family mutations.”  There has been consternation for some time about how to handle these types of situations.  ISOGG has set forth their criteria on their website.  They currently have the most comprehensive tree, but they certainly have their work cut out for them with the incoming tsunami of new SNPS that will be discovered utilizing these next generation tests, hundreds of which are currently in process.

STRs

A STR, or Short Tandem Repeat is analogous to a genetic stutter, or the copy machine getting stuck.  In the same situation as above, utilizing the same base for comparison, we see a group of inserted nucleotides that are all duplicates of each other.

STR example

In this case, we have a short tandem repeat that is 4 segments in length meaning that CT is inserted 4 times.  To translate, if this is marker DYS marker 390, you have a value of 5, meaning 5 repeats of CT.

So I’ve been fat and happy with this now for years, well over a decade.

The Monkey Wrench

And then I saw this:

“The L69/L159 polymorphism is essentially a SNP/STR oxymoron.”

To the best of my knowledge, this is impossible – one type of mutation excludes the other.  I googled about this topic and found nothing, nor did I find additional discussion of L69, other than this.

L69 verbiage

My first reaction to this was “that’s impossible,” followed by “Bloody Hell,” and my next reaction was to find someone who knew.

I reached out to Dr. David Mittelman, geneticist and Chief Scientific Officer at Gene by Gene, parent company of Family Tree DNA.  I asked him about the SNP/STR oxymoron and he said:

“This is impossible. There is no such thing as a SNP/STR.”

Whew!  I must say, I’m relieved.  I thought there for a minute there I had lost my mind.

I asked him what is really going on in this sequence, and he replied that, “This would be a complex variant — when multiple things are happening at once.”

Now, that I understand.  I have children, and grandchildren – I fully understand multiple things happening at once.  Let’s break this example apart and take a look at what is really happening.

HUGO is a reference standard, so let’s start there as our basis for comparison.

HUGO variant 1

In the L69 variant we have the following sequence.

HUGO variant 2

We see two distinct things happening in this sequence.  First, we have the deletion of two Gs, and secondly, we have the insertion of one additional TG.  According to Dr. Mittelman, both of these events are STRs, multiple insertions or deletions, and neither are point mutations or SNPs, so neither of these should really have SNP names, they should have STR type of names.

Let’s look at the L159 variant.

HUGO variant 3

In this case, we have the GG insertion and then we have a TG deletion.

In both cases, L69 and L159, the actual length of the DNA sequence remains the same as the reference, but the contents are different.  Both had 2 nucleotides removed and 2 added.

The good news is, as a consumer, that you don’t really need to know this, not at this level.  The even better news is that with the new discoveries forthcoming, whether they be STRs or SNPs, at the leafy end of the branch, they are often now overlapping with SNPs becoming much more genealogically useful.  In the past, if you were looking at a genetics mutation timeline, you had STRs that covered current to 1000 years, then nothing, then beginning at 5,000 or 10,000 years, you have SNPs that were haplogroup defining.

That gap has been steadily shrinking, and today, there often is no gap, the chasm is gone, and we’re discovering freshly hatched recently-occurring SNPs on a daily basis.

The day is fast approaching when you’ll want the full Y sequence, not to further define your haplogroup, but to further delineate your genealogy lines.  You’ll have two tools to do that, SNPs and STRs both, not just one.

I want to thank Dr. Mittelman for his generous assistance with this article.

What If You Die?

coffinWell, it’s not exactly a what-if question, it’s a given.  You’re going to.  The only real question is when, and will you be prepared?

By prepared, I’m not talking about your will, I’m talking about your DNA.

The unspeakable happened this past weekend.  A long time researcher and close friend, Aleda, died, rather unexpectedly.  She has been chronically ill for some time, but not critically.  On Saturday, she read my blog, worked with her research group on the Autosomal DNA Segment Analyzer and ordered Emily’s book.  Then, in the afternoon, she said she didn’t feel well and got into her chair to take a nap.  Nothing unusual about that.  Aleda didn’t feel well a lot, but she persevered anyway, always helping and guiding her research group.  But this time was different.  Aleda was gone.

Her research group is wandering around like a group of lost souls.  It’s like someone shot a hole through the middle of all of us.  This isn’t a large well organized group with an official structure, but a small group of closely and not so closely related researchers trying to figure out their DNA and genealogy connections.

If you are a significant contributor, you will be sorely missed.  If you are reading this, and have had your DNA tested, you are one of the contributors.

The research group members are already asking, “What next?  How do we access the DNA records of the people Aleda had tested?”  Good question.  Let’s talk about preparing for the inevitable.

Aleda had given the kit passwords to a friend, who is now so upset she can’t find them.  As the project administrator of one of the projects that includes one of Aleda’s family member’s kits, I can see some of the information.

E-Mail

I can see that Aleda set up a special DNA e-mail address which I’m presuming she used for all of the kits.  Unfortunately, there is no alternate e-mail address.

When Family Tree DNA, and virtually all the companies, do a password reset, they send the password information to the e-mail address on file.

Does anyone, other than Aleda, have the password to that e-mail account?

Project administrators cannot change primary e-mail addresses.  Only the kit owner can do that.

If you change your password to your e-mail account, you’ll need to remember to provide the new password to your trusted other as well.

Passwords

If you share your password with someone, that’s fine, but if they can’t find it, or if you change it and don’t tell them, that won’t be helpful.  You might want to add their e-mail as an alternate.  You might want to provide this information to multiple people, just in case your chosen person predeceases you, or some other unfortunate situation exists, like a fire, system crash or losing the passwords.

At 23andMe, to download a raw data file, a password isn’t enough.  You also have to know the answer to the secret question.

Beneficiary Information

Family Tree DNA goes one step further and provides people with a beneficiary form for situations just like this.

Unfortunately, Aleda’s family member’s form is blank, and she protected his information by changing the setting to prevent project administrators from completing this form.

beneficiary form

Covering all the Bases

Don’t forget about 3rd party sites like GedMatch where you may also be registered.

What to do?

1. Family Tree DNA is the only company to provide the option of beneficiary information.  Take advantage of this and complete the form.  It’s only 3 lines – name, phone and e-mail of your beneficiary.  You can find it under the “My Account” tab on the blue/black bar at the top of your personal page.

beneficiary dropdown

2. Add an alternate e-mail address.

3. Provide password and e-mail password information to a trusted other, and maybe a few trusted others.

4. Remember to notify password holders when you change passwords to either e-mail or DNA kits.

5. If you are a project administrator, try your best to find a co-administrator and share information, such as genealogy provided by participants.

6. Provide a notification list for your family that includes important genealogy and DNA contacts, including Family Tree DNA if you are a project administrator.  Many times I’ve received an e-mail from someone’s account with their name as the subject.  I’ve learned to cringe when I see them, because I know what’s coming…but at least the family has taken the trouble to notify those of us who communicate electronically with that person instead of leaving us to wonder forever what happened.

7. Preparing for the inevitable doesn’t just apply to DNA testing, but to all aspects of online life.  Think about Facebook, for example.  My brother died 2 years ago, today, and no one has his password.  We post to his page from time to time, but like a ghost ship, his Facebook account will sail off into the indefinite captainless future.

That Unruly X….Chromosome That Is

Iceberg

Something is wrong with the X chromosome.  More specifically, something is amiss with trying to use it, the way we normally use recombinant chromosomes for genealogy.  In short, there’s a problem.

If you don’t understand how the X chromosome recombines and is passed from generation to generation, now would be a good time to read my article, “X Marks the Spot” about how this works.  You’ll need this basic information to understand what I’m about to discuss.

The first hint of this “problem” is apparent in Jim Owston’s “Phasing the X Chromosome” article.  Jim’s interest in phasing his X, or figuring out where it came from genealogically, was spurred by his lack of X matches with his brothers.  This is noteworthy, because men don’t inherit any X from their father, so Jim’s failure to share much of his X with his brothers meant that he had inherited most of his X from just one of his mother’s parents, and his brothers inherited theirs from the other parent.  Utilizing cousins, Jim was able to further phase his X, meaning to attribute portions to the various grandparents from whence it came.  After doing this work, Jim said the following”

“Since I can only confirm the originating grandparent of 51% my X-DNA, I tend to believe (but cannot confirm at the present) that my X-chromosome may be an exact copy of my mother’s inherited X from her mother. If this is the case, I would not have inherited any X-DNA from my grandfather. This would also indicate that my brother Chuck’s X-DNA is 97% from our grandfather and only 3% from our grandmother. My brother John would then have 77% of his X-DNA from our grandfather and 23% from our grandmother.”

As a genetic genealogist, at the time Jim wrote this piece, I was most interested in the fact that he had phased or attributed the pieces of the X to specific ancestors and the process he used to do that.  I found the very skewed inheritance “interesting” but basically attributed it to an anomaly.  It now appears that this is not an anomaly.  It was, instead the tip of the iceberg and we didn’t recognize it as such.  Let’s look at what we would normally expect.

Recombination

The X chromosome does recombine when it can, or at least has the capacity to do so.  This means that a female who receives an X from both her father and mother receives a recombined X from her mother, but receives an X that is not recombined from her father.  That is because her father only receives one X, from his mother, so he has nothing to recombine with.  In the mother, the X recombines “in the normal way” meaning that parts of both her mother’s and her father’s X are given to her children, or at least that opportunity exists.  If you’re beginning to see some “weasel words” here or “hedge betting,” that’s because we’ve discovered that things aren’t always what they seem or could be.

The 50% Rule

In the statistical world of DNA, on the average, we believe that each generation receives roughly half of the DNA of the generations before them.  We know that each child absolutely receives 50% of the DNA of both parents, but how the grandparents DNA is divided up into that 50% that goes to each offspring differs.  It may not be 50%.  I am in the process of doing a generational inheritance study, which I will publish soon, which discusses this as a whole.

However, let’s use the 50% rule here, because it’s all we have and it’s what we’ve been working with forever.

In a normal autosomal, meaning non-X, situation, every generation provides to the current generation the following approximate % of DNA:

Autosomal % chart

Please note Blaine Bettinger’s X maternal inheritance chart percentages from his “More X-Chromosome Charts” article, and used with his kind permission in the X Marks the Spot article.

Blaine's maternal X %

I’m enlarging the inheritance percentage portion so you can see it better.

Blaine's maternal X % cropped

Taking a look at these percentages, it becomes evident that we cannot utilize the normal predictive methods of saying that if we share a certain percentage of DNA with an individual, then we are most likely a specific relationship.  This is because the percentage of X chromosome inherited varies based on the inheritance path, since men don’t receive an X from their fathers.  Not only does this mean that you receive no X from many ancestors, you receive a different percentage of the X from your maternal grandmother, 25%, because your mother inherited an X from both of her parents, versus from your paternal grandmother, 50%, because your father inherited an X from only his mother.

The Genetic Kinship chart, below, from the ISOGG wiki, is the “Bible” that we use in terms of estimating relationships.  It doesn’t work for the X.

Mapping cousin chart

Let’s look at the normal autosomal inheritance model as compared to the maternal X chart fan chart percentages, above, and similar calculations for the paternal side.  Remember, the Maternal Only column applies only to men, because in the very first generation, men’s and women’s inheritance percentages diverge.  Men receive 100% of their X from their mothers, while women receive 50% from each parent.

Generational X %s

Recombination – The Next Problem

The genetic genealogy community has been hounding Family Tree DNA incessantly to add the X chromosome matching into their Family Finder matching calculations.

On January 2, 2014, they did exactly that.  What’s that old saying, “Be careful what you ask for….”  Well, we got it, but “it” doesn’t seem to be providing us with exactly what we expected.

First, there were many reports of women having many more matches than men.  That’s to be expected at some level because women have so many more ancestors in the “mix,” especially when matching other women.

23andMe takes this unique mixture into consideration, or at least attempts to compensate for it at some level.  I’m not sure if this is a good or bad thing or if it’s useful, truthfully.  While their normal autosomal SNP matching threshold is 7cM and 700 matching SNPs within that segment, for X, their thresholds are:

  • Male matched to male – 1cM/200 SNPs
  • Male matched to female – 6cM/600 SNPs
  • Female matched to female – 6cM/1200 SNPs

Family Tree DNA does not use the X exclusively for matching.  This means that if you match someone utilizing their normal autosomal matching criteria of approximately 7.7cM and 500 SNPs, and you match them on the X chromosome, they will report your X as matching.  If you don’t match someone on any chromosome except the X, you will not be reported as a match.

The X matching criteria at Family Tree DNA is:

  • 1cM/500 SNPs

However, matching isn’t all of the story.

The X appears to not recombine normally.  By normally, I don’t mean something is medically wrong, I mean that it’s not what we are expecting to see in terms of the 50% rule.  In essence, we would expect to see approximately half of the X of each parent, grandfather and grandmother, passed on to the child from the mother in the maternal line where recombination is a possibility.  That appears to not be happening reliably.  Not only is this not happening in the nice neat 50% number, the X chromosome seems to be often not recombining at all.  If you think the percentages in the chart above threw a monkey wrench into genetic genealogy predictions, this information, if it holds up in a much larger test, in essence throws our predictive capability, at least as we know it today, out the window.

The X Doesn’t Recombine as Expected

In my generational study, I noticed that the X seemed not to be recombining.  Then I remembered something that Matt Dexter said at the Family Tree DNA Conference in November 2013 in Houston.  Matt has the benefit of having a full 3 generation pedigree chart where everyone has been tested, and he has 5 children, so he can clearly see who got the DNA from which of their grandparents.

I contacted Matt, and he provided me with his X chromosomal information about his family, giving me permission to share it with you.  I have taken the liberty of reformatting it in a spreadsheet so that we can view various aspects of this data.

Dexter table

First, note that I have sorted these by grandchild.  There are two females, who have the opportunity to inherit from 3 grandparents.  The females inherited one copy of the X from their mother, who had two copies herself, and one copy of the X from her father who only had his mother’s copy.  Therefore, the paternal grandfather is listed above, but with the note “cannot inherit.”  This distinguishes this event from the circumstance with Grandson 1 where he could inherit some part of his maternal grandfather’s X, but did not.

For the three grandsons, I have listed all 4 grandparents and noted the paternal grandmother and grandfather as “cannot inherit.”  This is of course because the grandsons don’t inherit an X from their father.  Instead they inherit the Y, which is what makes them male.

According to the Rule of 50%, each child should receive approximately half of the DNA of each maternal grandparent that they can inherit from.  I added the columns, % Inherited cM and % Inherited SNP to illustrate whether or not this number comes close to the 50% we would expect.  The child MUST have a complete X chromosome which is comprised of 18092 SNPs and is 195.93cM in length, barring anomalies like read errors and such, which do periodically occur.  In these columns, 1=100%, so in the Granddaughter 1 column of % Inherited cM, we see 85% for the maternal grandfather and about 15% for the maternal grandmother.  That is hardly 50-50, and worse yet, it’s no place close to 50%.

Granddaughter 1 and 2 must inherit their paternal grandmother’s X intact, because there is nothing to recombine with.

Granddaughter 2 inherited even more unevenly, with about 90% and 10%, but in favor of the other grandparent.  So, statistically speaking, it’s about 50% for each grandparent between the two grandchildren, but it is widely variant when looking at them individually.

Grandson 1, as mentioned, inherited his entire X from his maternal grandmother with absolutely no recombination.

Grandsons 2 and 3 fall much closer to the expected 50%.

The problem for most of us is that you need 3 or 4 consecutive generations to really see this happening, and most of us simply don’t have data that deep or robust.

A recent discussion on the DNA Genealogy Rootsweb mailing list revealed several more of these documented occurrences, among them, two separate examples where the X chromosome was unrecombined for 4 generations.

Robert Paine, a long-time genetic genealogy contributor and project administrator reported that in his family medical/history project, at 23andMe, 25% of his participants show no recombination on the X chromosome.  That’s a staggering percentage.  His project consists of  21 people in with 2 blood lines tested 5 generations deep and 2 bloodlines tested at 4 generations

One woman’s X matches her great-great-grandmother’s X exactly.  That’s 4 separate inheritance events in a row where the X was not recombined at all.

The graphic below, provided by Robert,  shows the chromosome browser at 23andMe where you can see the X matches exactly for all three participants being compared.

The screen shot is of the gg-granddaughter Evelyn being compared to her gg-grandmother, Shevy, Evelyn’s g-grandfather Rich and Evelyn’s grandmother Cyndi. 23andme only lets you compare 3 individuals at a time so Robert did not include Evelyn’s mother Shay, who is an exact match with Evelyn.

Paine X

Where Are We?

So what does this mean to genetic genealogy?  It certainly does not mean we should throw the baby out with the bath water.  What it is, is an iceberg warning that there is more lurking beneath the surface.  What and how big?  I can’t tell you.  I simply don’t know.

Here’s what I can tell you.

  • The X chromosome matching can tell you that you do share a common ancestor someplace back in time.
  • The amount of DNA shared is not a reliable predictor of how long ago you shared that ancestor.
  • The amount of DNA shared cannot predict your relationship with your match.  In fact, even a very large match can be many generations removed.
  • The absence of an X match, even with someone closely related whom you should match does not disprove a descendant relationship/common ancestor.
  • The X appears to not recombine at a higher rate than previously thought, the previous expectation being that this would almost never happen.
  • The X, when it does recombine appears to do so in a manner not governed by the 50% rule.  In fact, the 50% rule may not apply at all except as an average in large population studies, but may well be entirely irrelevant or even misleading to the understanding of X chromosome inheritance in genetic genealogy.

The X is still useful to genetic genealogists, just not in the same way that other autosomal data is utilized.  The X is more of an auxiliary chromosome that can provide information in addition to your other matches because of its unique inheritance pattern.

Unfortunately, this discovery leaves us with more questions than answers.  I found it incomprehensible that this phenomenon has never been studied in humans, or in animals, for that matter, at least not that I could find.  What few references I did find indicated that the X seems to recombine with the same frequency as the other autosomes, which we are finding to be untrue.

What is needed is a comprehensive study of hundreds of X transmission events at least 3 generations deep.

As it turns out, we’re not the only ones confused by the behavior of the X chromosome.  Just yesterday, the New York Times had an article about Seeing the X Chromosome in a New Light.  It seems that either one copy of the X, or the other, is disabled cell by cell in the human body.  If you are interested in this aspect of science, it’s a very interesting read.  Indeed, our DNA continues to both amaze and amuse us.

A special thank you to Jim Owston, Matt Dexter, Blaine Bettinger and Robert Paine for sharing their information.

Additional sources:

Polymorphic Variation in Human Meiotic
Recombination (2007)
Vivian G. Cheung
University of Pennsylvania
http://repository.upenn.edu/cgi/viewcontent.cgi?article=1102&context=be_papers

A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome, Science October 2005, Myers et al
http://www.sciencemag.org/content/310/5746/321.full.pdf
Supplemental Material
http://www.sciencemag.org/content/suppl/2005/10/11/310.5746.321.DC1

The $1000 Genome? – Not Exactly

HiSeqXTen

You may have seen the headlines and the announcement this week by Illumina, manufacturer of gene sequencing equipment, that the $1000 genome is finally here.  Hallelujah –  jump for joy – right?  Sign me up – where can I order???

Well, not so fast.

It’s a great headline – and depending on how you figure the math – it’s not entirely untrue, but it’s a real struggle to get there.  Some marketing maven did some real spreadsheet magic!  What is that old saying, “lies, damned lies and statistics”?  Maybe that’s a little harsh, but it’s not too far off.

So, is the $1000 genome here or not?  Well, kindof.  It depends on how you count, and who you are.  You see, it’s a math thing.

It’s kind of like a mortgage.  How much did your house cost?  Let’s say $100,000 – that was the price on the “for sale” sign.  But by the time you get the mortgage paid off, 30 years later, the cost of that house is way more than $100,000, probably more than $250,000 and if you add in the cost of taxes, closing costs and maintenance, even more.  This will only depress you, so don’t think about, especially when you sell your house for $150,000 and declare that you “made” $50,000.  But I digress…

So, let’s translate this to the $1000 genome.

Dr. David Mittleman, Chief Scientific Officer for Gene by Gene, Ltd., parent company of Family Tree DNA, was at the conference this week where the Illumina announcement was made. I asked him several questions about this new technology and if it was ready for prime time yet.

His first comment shed some light on costs.

“The HiSeqX Ten system is actually a ten-pack of new HiSeq instruments, each costing 1 million dollars. So you have to spend $10 million on equipment before you can even get started.”

Ouch.  I guess I won’t be buying one anytime soon!

To begin with, without the cost of the kits or processing or staff or software or installation or financing or support contracts or profit, a company would have to sell 10,000 kits at $1000 to even bring the cost of the equipment to $1000 per kit.

So, how did Illumina figure the cost of the $1000 genome?  The $1000 is broken down as $800 on reagents, $135 on equipment depreciation over 4 years, and $65 on staff/overheads.

This means that to obtain that $1000 per genome price, you have to run the equipment at full capacity, 24X7, 18,000 kits per year, for 4 full years.  And that still doesn’t include everything.  You also need service contracts, installation, additional labor, etc.  You can read more about the math and cost of ownership here.

And sure enough, when I asked David about who has purchased one so far, there are two buyers and both are institutions.  This is an extremely high end product, not something for the DTC consumer marketspace.

Now this isn’t to say this announcement is a bad thing – it’s not – it’s just not exactly what the headlines suggest.  It’s the $1000 genome for those with deep pockets who can purchase a $10,000,000 piece of gear and then run 18,000 samples, for 4 years, plus expenses.  But yes, it does technically break down to $1000 per test as long as you hit all of those milestones and ignore the rest of the expenses.  If you can afford $10 million and have the staff to run it, you probably don’t care about the cost of installation, labor and support contracts.  They are just necessary incidentals – like gas for my lawn mower!

In spite of the fancy math, it’s truly amazing how far we’ve come when you consider that a single full genome sequence still cost about 3 million in 2007, and in November 2012 Gene by Gene was the first to offer full sequencing commercially and offered it to their customers for an introductory price of $5495.  Of course, with no analysis tools and few testers, I can’t imagine what one would do with those results.  This has changed somewhat today.  The full genome with some analysis is available today to consumers for $7595, but the question of what is available that is genealogically useful to do with these results still remains, and will, until many more people test and meaningful comparisons are available.

The Illumina announcement also raises the issue of software investment to do something useful with the massive amount of data this new equipment will generate…also nontrivial, and that software does not exist yet today.

There are other issues to be addressed as well, like open access libraries.  Will they exist?  If so, where?  Who cares for them?  How are they funded?  Who will have access?  Will this data be made available in open access libraries, assuming they exist?

Illumina has reported that entire countries have approached them asking for their population to be sequenced, which also begs questions of privacy, security and how exactly to anonymize the samples without them becoming useless to research.  This high tech watershed announcement may spur as many questions as answers, but these issues need to be resolved in the academic environment before they trickle down to the consumer marketspace.

This is not to minimize the science and technology that has propelled us to this breakthrough.  It is a wonderful scientific and technological advancement because it will allow governments or large institutes to do huge population-wide studies.  This is something we desperately need.  Think for a minute if our Population Finder ethnicity results were based on tens of thousands of samples instead of selected hundreds.

For genetic genealogists, we are poised to benefit in the future, probably the more distant than the near future.  The $1000 genome for consumers not only isn’t here, it’s not even within sniffing distance.  So put your checkbooks away or better yet, buy a Big Y or a Family Finder test for a cousin, something that will benefit you in the short term.

This next step in the world of genetic discovery is exciting for research institutes, but it’s not yet ready for consumer prime time.  We will be the beneficiaries, but not the direct consumers….yet…unless you want to move to one of those countries who wants their entire population sequenced.  Our turn will come.  Maybe the next time we see an announcement for the $1000 genome it will be calculated in normal home-owning-human terms.

If you’d like to see the product announcement and a cool video that Illumina created, take a look here.  The video is short and provides a neat way to look at genetic history.

Introducing the Autosomal DNA Segment Analyzer

We have a brand new toy in our DNA sandbox today, thanks to Don Worth, a retired IT professional.  I just love it when extremely talented people retire and we, in the genetic genealogy community, are the benefactors of their Act 2 evolution.  Our volunteers make such a cumulative difference.

Drum Roll please.

Introducing…..the Autosomal DNA Segment Analyzer, or ADSA.

The name alone doesn’t make your heart skip beats, but the product will.  This tool absolutely proves the adage that a picture is worth 1000 words.

Don described his new tool, which, by the way, is free and being hosted by Rob Warthen at www.dnagedcom.com, thus:

I created this tool in an attempt to put all the relevant information available that was needed to evaluate segment matches on a single, interactive web page. It relies on the three files for a single test kit that DNAgedcom.com collects from FamilyTreeDNA.com. These files include information about your matches, matching segment locations and sizes, and “in common with” (ICW) data. Using these files, the tool will construct a table for each chromosome which includes match and segment information as well as a visual graph of overlapping segments, juxtiposed with a customized, color-coded ICW matrix that will permit you to triangulate matching segments without having to look in multiple spreadsheets or on different screens in FamilyTreeDNA. Additional information, such as ancestral surnames, suggested relationship ranges, and matching segments and ICWs on other chromosomes is provided by hovering over match names or segments on the screen. Emails to persons you match may also be generated from the page. The web page produced by this program does not depend on any other files and may be saved as a stand-alone .html file that will function locally (or offline) in your browser. You can even email it to your matches as an attachment. You can play with a working sample output here.

Who wants to play with sample output?  I wanted to jump right in.  Word of caution…read the instructions FIRST, and pay attention, or you’ll wind up downloading your files twice.  The instructions can be found here.

I can’t tell you how many times, when I’ve been working with matches, that I’ve wondered to myself, “How many other people match us on this segment?”  For quite a while you could only download 5 people at a time, but now you can download the entire data file.  I’m a visual person.  To me, visually seeing is believing and the ADSA makes this process so much easier.  Truly, a picture is worth 1000 words.

I knew right away there were three things I wanted to do, so I’m going to run through each one of the three by way of examples to illustrate what you can do with the power of this wonderfully visual tool.  I’ve also anonymized the matches.

1. Clusters of matches.

I know I’ve told you that I’m mapping my DNA to ancestors.  When I first saw Don’s output, I knew immediately that this tool would be invaluable for grouping people from the same ancestral lines.

Barbara, the second row, is my mother and her DNA in this equation is extremely useful.  It helps me identify right away which side of my family a match comes from.  If you don’t have a parent available, aunts, uncles, cousins, all help, especially cumulatively.

Before we begin working with the results, take a minute and just sit and look at the graphic below.  These two clusters shown on this page, one near the top and the other at the bottom….they represent your ancestors.  Two very different ones in this case. This may be the only way you’ll ever “see” them, by virtue of a group of their descendants DNA clustered together.  A view through the keyhole of time provided by DNA. Isn’t it beautiful?

adsa cluster 1

All of these results in this “cluster of matches” example are my matches.  In other words, the file is mine and these are people who are matching me.  You can see that this tool provides us with start and end segments, total cMs and SNPs, and e-mails, but the true power is in the visual representation of the ICW (in common with) matrix.  The mapped segments are a nice touch too, and Don has listed these in progressive order, meaning from beginning to end of the segment (left to right.)

Look at this initial clustered group, shown enlarged below.  The first individual matches me and mother on one pink segment, but matches me on two segments, a pink and a black.  That means he’s from Mom’s side, or at least through one line, but probably somewhat distant since that one segment is his only match on any chromosome.  Because he also matches me on a segment where he doesn’t match Mom, he could also be related to me on my father’s side, or maybe we had a misread error on the black segment when comparing to Mom’s DNA. It is the adjoining segment.  In essence, there isn’t enough information to do much with this, except ask questions, so let’s move on to something more informative.

Beginning with the third person, the next grouping or cluster is entirely non-matching to mother, so this entire cluster is from my father’s side AND related to each other.

There are 6 solid matches here, and then they start to trail off to matches that aren’t so solid.

ADSA cluster 1 A

By flying over the match names with my cursor, I might be able to tell, based on their surnames, which line is being represented by this cluster of matches.  If I already have a confirmed cousin match in the group, then the rest of the group can be loosely attributed to that line, or a contributing (wife) line. Unfortunately, in this case, I can’t tell other than it looks like it might be through Halifax County, VA.  I do have an NPE there and some wives without surnames.

Let’s look on down this chromosome.  There is another very solid cluster, also on my Dad’s side.  In this second cluster, I have identified a solid cousin and I can tell you that this is a Crumley grouping.  My common ancestor with my Crumley cousin is William Crumley born about 1765 in Frederick Co., Va. and who died about 1840 in Lee Co., Va.  His wife is unknown, but we have her mitochondrial DNA.  Now this doesn’t mean that everyone in this group will all have a Crumley ancestor, they may not.  They may instead have a Mercer, a Brown, a Johnson or a Gilkey, all known wives’ surnames of Crumley men upstream of William Crumley.  But someplace, there is a common ancestor who contributed quite a bit of chromosome 1 to a significant number of descendants, and at least two of them are Crumleys.

ADSA Crumley cluster

At first, I found it really odd that my mother had almost no matches with me on chromosome 1.  Some of my mother’s ancestors came to the States later, from the Netherlands and from Germany.  Many of these groups are under-represented in testing.  However other ancestral groups have been here a long time, Acadians and Brethren Germans.  My father’s Appalachian, meaning colonial, ancestors seem to have more descendants who have tested.

However, looking now at chromosome 9, we see something different.

ADSA Acadian cluster

The second person, Doris, doesn’t match Mom anyplace, so is obviously related through my father, but look at that next grouping.

I can tell you based on hovering over the matches name that this is an Acadian grouping.  The Acadians are a very endogamous French-Canadian group, having passed the same DNA around for hundreds of years.  Therefore, a grouping is likely to share a large amount of common DNA, and this one does.

ADSA Acadian flyover

Based on this, I can then label all of these various matches as “Acadian” if nothing more.

Within a cluster, if I can identify one common ancestor, I can attribute the entire large group to the same lineage.  Be careful with smaller groups or just one or two rectangle matches.  Those aren’t nearly as strong and just because I match 2 people on the same segment doesn’t mean they match each other. However, when you see large segments of people matching each other, you have an ancestral grouping of some sort.  The challenge of course is to identify the group – but a breakthrough with one match means a likely breakthrough with the rest of them too, or at least another step in that direction.

2. Source of DNA

I have several cousins who match me on two or more distinct lines.  This tool makes it easy, in some cases, to see which line the DNA on a particular chromosome comes from.

I have both Claxton (James Lee Claxton/Clarkson born c 1775-1815 and Sarah Cook of Hancock Co., TN)  and Campbell (John Campbell b c 1772-1838 and Jane Dobkins born c 1780-1850/1860 of Claiborne Co., Tn.) ancestry.  My cousins, Joy and William do too.  In this case, you can see that Joy matches a Claxton (proven by Y DNA to be from our line) and so does William on the first green matching segment.  The second green segment is not found in the Claxton match, so it could be Claxton and the Claxton cousin didn’t receive it, or it could be Campbell, but it’s one or the other because Joy, William and I all three carry this segment.

ADSA Claxton Campbell

What this means is that the light green segments are Claxton segments, as are the fuchsia segments.  The source of the darker green segment is unknown.  It could be either Claxton or Campbell or a third common line that we don’t know about.

3.  Untangling Those Darned Moores

I swear, the Moore family is going to be the death of me yet. It’s one of my long-standing, extremely difficult brick walls.  It seems like every road of every county in Virginia and NC had one or more Moore families.  It’s a very common name.  To make thing worse, the early Moores were very prolific and they all named their children the same names, like James and William, generation after generation.

The earliest sign I can find of my particular Moore family is in Prince Edward County, Virginia when James Moore married Mary Rice (daughter of Joseph Rice and wife Rachel) in the early 1740s.  By the 1770s, the family was living in Halifax County, Virginia and their children were marrying and having children of their own of course.  They were some of the early Methodists with their son, the Reverend William Moore being a dissenting minister in Halifax County and his brothers Rice and Mackness Moore doing the same in Hawkins and Grainger County, TN.  Another son, James, went to Surry Co., NC.  We have confirmed this with a DNA descendant match.

We have the DNA of our Moore line proven on the Y side through multiple sons.  At the Moore Worldwide DNA project, we are group 19.  Now there are Moores all over the place in Halifax County.  I know, because I’ve paid for about half of them to DNA test and there are several distinct lines – far more than I expected.  Ironically, the Anderson Moore family who lived across the road from our James and then his son Rev. William, who raised the orphan Raleigh Moore, grandson of the Rev. William Moore, is NOT of the same Moore DNA line.  Based on the interaction of these two families, one would think assuredly that they were, which raises questions.  This Anderson Moore was the son of yet another James Moore, this one from Amelia County, VA., found in the large group 1 of the Moore project.  If this is all just too confusing and too close for comfort for you, well, join the crowd and what we Moore descendants have been dealing with for a decade now.

This raises the question of why there are so few matches to our Moore line.  Was our Moore line a “new Moore line,” born perhaps to a Moore daughter who gave the child her surname.  However, the child of course would pass on the father’s Y chromosome, establishing a “new” Moore genetic line.  I’m not saying that is what happened, just that it’s odd that there are so few matches to a clearly colonial Moore line out of Virginia.  With only one exception, someone genealogically stuck in Kentucky, to date, all DNA matches are all descendants of our James.  We do know that there was a William Moore, wife Margaret, living adjacent to James Moore in Prince Edward County but he and his wife sold out and moved on and are unaccounted for.

I’ve seen this same pattern with the Younger family line too, and sure enough, we did prove that these two different Y chromosome Younger families in fact do share a common ancestor.

So you can see why I get excited when I find anything at all, and I mean anything, about the Moore family line.

A Moore descendant of Raleigh, the orphan, has taken the autosomal Family Finder test, and he matched my cousin Buster, a known Moore descendant, and also another Cumberland Gap region researcher, Larry.  Larry also matches Buster.  I was very excited to see this three way match and I wrote to Larry asking if he had a Moore line.  Yes, he did, two in fact.  The Levi Moore line out of Kentucky and an Alexander Moore line out of Stokes County, NC, after they wandered down from Berks Co., PA. sometime before 1803.

Groan. Two Moores – I can’t even manage to sort one out, how will I ever sort two?

Then Larry told me that he had 4 of his cousins tested too.  Bless you Larry.

And better yet, one of Larry’s Moore lines is on his mother’s side and one on his father’s.  Even better yet.  Things are improving.

Now I’m really excited, right up until I discover that my cousin Buster matches two of Larry’s 3 cousins on his mother’s side and my Moore cousin from Halifax County, Virginia, matches the cousin on Larry’s father’s side.

How could I be THIS unlucky???

So I started out utilizing the ICW and Matrix tools at Family Tree DNA.  Because these people all matched Larry on overlapping segments on the chromosome browser, my first thought was maybe that these two Moore lines were really one and the same.  But then I pushed the ICW matches through to the Family Finder Matrix, and no, Larry’s paternal cousin does not match any of the three maternal cousins, who all match each other.  So the two Moore families are not one and the same.

Crumb.  Thank Heavens though for the Matrix which provides proof positive of whether your matches match each other.  Remember, you have two sides to each chromosome and you will have matches to both sides.  Without the Matrix tool, you have no way of knowing which of your matches are from the same side of your chromosome, meaning Mom’s side or Dad’s side.

Just about this time, as I was beginning to construct matrixes of who matches whom in the ICW compares between all of the ICW match permutations, I received a note from Don that he wanted beta testers for his new ADSA application.  I immediately knew what I was going to test!

I started with my cousin Buster’s kit.  Buster is one generation upstream from me, so one generation closer to the Moore ancestors.

On Larry’s maternal line, descended from the Levi Moore (Ky) line, he tested three cousins.  Buster had the following match results with Larry and his maternal line cousins.

  • Larry – match
  • Janice  – no match
  • Ronald  – match
  • B.J.  – match

I have redacted the e-mails and surnames below, but want to draw your attention to the individuals with the red arrows, as noted above.ADSA1 cropped v2

On the graphic below, I’m showing only the right side, so you can see the matching ICW (in common with) block patterns.  Larry is last, I’m second from last and Larry’s two cousins are the first and second red arrows.  We are all matching to my cousin, Buster.

ADSA2 cropped

You can see that all of these people match Buster.  Larry has blocks that are pink, red, fuchsia, gold, navy blue and lime green.  All of the group above, except me and two other people, one of which is my known cousin on another line, match Larry on these blocks, or at least most of these blocks.  I, however, match none of this group on none of these blocks, nor do my other known cousins who also descend through this same Moore line.  This means that this group matches Buster through Buster’s mother’s line, not through the Estes line, which means that this Moore line is not the James Moore line of Halifax County.  So the Levi Moore group of Kentucky is not descended from the James Moore group of Prince Edward and Halifax County.

Of course, I’m disappointed, but eliminating possibilities is just as important as confirming them.  I keep telling myself that anyway.

The male Moore descendant in Halifax Co., proven via Y line testing, does match with Chloa, Larry’s paternal cousin, and with Larry as well, as shown below.  Let’s see if we can discern any other people who match in a cluster, which would give us other people to contact about their Moore lines.  Keep in mind that we don’t know that the DNA in common here is from the Moore line.  It could come from another common line.  That is part of what we’d like to prove.

ADSA3

Let’s take a closer look at what this is telling us.

First, there’s a much smaller group, and this is the only chromosome where Chloa matches our Moore cousin.

So let’s look at each line.  The first person, John, doesn’t match anyone else, so he’s not in this group.

Larry and his cousin, Chloa are second and third from the bottom, and they form the match group.  You can see that they match exactly except Chloa has one brighter green segment that matches our Moore cousin in a location with no other matches.  However, the match group of navy blue, periwinkle, lime green and burgundy form a distinctive pattern.  In addition to Chloa and Larry, Virginia, and Arlina share the same segments, plus Arlina had a pink segment that Larry and Chloa don’t have.  Donald may be a cousin too, but we don’t know if Donald would also match the rest of the group.  Linda might match Donald, but doesn’t look like she matches the group, but she could.  At this point, we can drop back to Family Tree DNA and the matrix and take a look to see if these folks match each other in the way we’d expect based on the ADSA tool.

ADSA Matrix

Just like we expected, John doesn’t match anyone.  As expected, Larry, Chloa, Arlina, and Virginia all matched each other.  As it turns out, Linda does not match the rest of the group, but she does match Donald, who does match Arlina.  Therefore, our focus needs to be on contacting Arlina, Donald and Virginia and asking them about their Moore lines, or the surnames of known Moore wives, such as Rice in my James Moore line or wives surnames in Larry’s Moore line.  Just on the basis of possibility, I would also contact Linda and ask, but she is the long shot.  However, like the lottery, you can’t win if you don’t play, so just send that one extra e-mail.  You never know.  Life is made up of stories about serendipity and opportunities almost missed.

If Larry’s Moore line is the same as our Moore cousin’s line, genetically, maybe we can make headway by tracking Larry’s line.  Larry was kind enough to provide me with a website, and his Moore line begins with daughter Sarah.  Her father is Alexander Moore born in 1730 who married Elizabeth Wright.  His father was Alexander born in 1710 and who lived in Bucks Co., PA.  The younger Alexander died in Stokes Co., NC in 1803.

Moore website 1 cropped

Moore website 2

Moore website 3

Our next step is to see if this Alexander Moore line has been Y DNA tested.  Checking back at the Moore Worldwide project, this family line is not showing, but I’ve dropped a note to the administrators,  just the same.  Unfortunately, not everyone enters their most distant ancestor information which means that information is blank on the project website.

If this Alexander Moore line has been Y tested, then we already know they don’t match our group paternally.  The connection, in that case, if this genetic connection is a Moore line, could be due to a daughter birth.  If this Moore line has not been Y tested, then it means that I’ll be trying to track down a Moore descendant of one of these Alexander Moores to do the DNA test.  It would be wonderful to finally make some headway on the James Moore family.  We’ve been brick walled for such a long time.

If you descend from either of these Moore family lines, the James Moore (c 1720-c 1798) and Mary Rice line, or the Alexander Moore and Elizabeth Wright or Elizabeth Robinson line, please consider taking the Family Finder autosomal DNA test at Family Tree DNA.  If you know of a male Moore who descends from the Alexander Moore line, let’s see if he would be willing to Y DNA test.

There is a great deal of power in the combined results of descendants, as you can clearly see, thanks to Don Worth and his new Autosomal DNA Segment Analyzer tool.

Give it a test run at: http://www.DNAgedcom.com/adsa

Don wrote documentation and instructions, found here.  Please read them before downloading your files.

And Don, a big, hearty thank you for this new way to “see” our ancestors!  Thank you to Rob Warthen too for hosting this wonderful new tool!

X-Chromosome Matching at Family Tree DNA

Just as they promised, and right on schedule, Family Tree DNA today announced X chromosome matching.  They have fully integrated X matching into their autosomal Family Finder product matching.  This will be rolling live today.  Happy New Year from Family Tree DNA!!!

In the article, X Marks the Spot, I showed the unique inheritance properties of the X chromosome.  In a nutshell, men only inherit one copy from their mother, because they inherit a Y from their father, but women get a copy from both parents.  Still, you don’t inherit parts of your X from all of your ancestors, so knowing your own X inheritance pattern can help immensely to rule out common genealogy lines when you match someone on the X.

In their informational rollout, Family Tree DNA provided the following information about their new features.

Here is the menu link to the Family Finder Matches menu.

x match 1

On the Family Finder Matches page, there is a filter to show only X-Matches.

x match 2

When you use the X-Match filter on a male Family Finder kit, you should get only matches from the maternal X-Chromosome.

x match 3

Next, like other Family Finder Matches you can expand the advanced bar for a match and click to add the match to the Compare in Chromosome Browser list.

x match 4

Matches are added to the Compare in Chromosome Browser list. You could go right to the Chromosome Browser by clicking on the compare arrow at this point.

x match 5

Next we can also go right to the Chromosome Browser.

x match 6

The Chromosome Browser also lets you filter the match list by X-Matches.

x match 7

Here are three immediate relatives. The first two share X-Chromosome DNA. The third (green) one does not.

x match 8

When we scroll down to the X at the bottom, we see that X-Matching is displayed for the first two but not the third.

x match 9

Moving to the Advance Matching page, X-Chromosome matches have also been integrated.

x match 10

X-Match is an option that can be checked alongside other types of testing.

x match 11

Promethease – Genetic Health Information Alternative

People are beginning to ask about how they can obtain some of the health information that they were previously receiving from 23andMe.  For $5, at Promethease,  you can upload any of the autosomal files from either Family Tree DNA, 23andMe or Ancestry.com.  They will process your raw data and provide you with a report that is available to download from their server for 45 days.  They also e-mail you a copy.

At Promethease, your raw data file is deleted within 24 hours of completion of your report, and your report file will be deleted after 45 days, so be sure to download your report for future reference.  Currently they process about 20,000 genotypes, or SNPs.  They do note that they update their data base regularly from SNPedia, fed from PubMed publications.  Therefore your report in the future will include SNPs that won’t be in your report today and what we’ve learned about those SNPs may differ as well.

They have also noted that you receive different items in your report based on which vendor’s full data file you submit.  That’s true.  I uploaded all 3 of my raw data files, from Ancestry, 23andMe and Family Tree DNA and ran Promethease against each of them.  While 23andMe optimized their chip for medical and health results, Family Tree DNA intentionally removed some medically relevant data in order to avoid any FDA type of issues.  It’s unknown how Ancestry treats medically significant SNPs, but I’m running all 3 vendor’s files to view differences.

  • The Promethease report utilizing the 23andMe raw data file reported on 20,080 genotypes.
  • The Promethease report utilizing the Family Tree DNA raw data file reported on 8179 genotypes.
  • The Promethease report utilizing the Ancestry raw data file reported on 10,498 genotypes.

To start the process of uploading your file and running your report, visit:

https://promethease.com/ondemand

Of course, you’ll need to take care of housekeeping, sign up and pay.

You will then be asked to select an ethnicity.  I always hate this question, because I’m more than one and the categories never fit.  If you don’t fit any category well, select the closest.   Promethease says it only affects the sort order.  That was a relief to me, as I always wonder what I’m missing by making one selection over another.

While the report actually runs, which takes about 15-20 minutes, amuse yourself by watching the video about how to download, read and understand your results.  Or you could write a blog, like me!

Promethease instructional video

You can review this video at any time by visiting the original link.  It does make more sense after you have your report in hand.

My report only took 8 minutes to run, and according to the front page of my report, they analyzed over 20,000 SNPs or known mutation locations.  I’m excited to see what my report holds.

One of the reasons I’ve been interested in this type of DNA reporting is that my mother was “diagnosed” with Parkinson’s Disease. I put diagnosed in quotes, because Parkinson’s is a diagnosis of exclusion, for which there is no specific diagnostic test, meaning the diagnosis is one made after other alternative diseases for which there are tests, are excluded.  However, she never had some of the traditional symptoms, like the specific walking gait typical in Parkinson’s patients, nor some of the other symptoms, nor were the Parkinson’s medications effective in controlling her hand tremors. Her father also had the same tremors, which I’ve always suspected was Familial Tremor, not Parkinson’s.  I wanted to see if Mom or I carried elevated risk for Parkinson’s.  Mom’s DNA was archived at Family Tree DNA, so I could run the Family Finder test even though she had passed away by the time autosomal testing was available.  So I uploaded and ran her file at Promethease too, and compared with my own.

So, let’s look at my report based on the 23andMe raw data file.

Promethease report

At this point, you have to choose to click on “Bad News” or “Good News” first.  Someone should do a study about whether you select bad or good is genetically influenced.

In my case, I was interested to see if my “bad news” was the same “bad news” that 23andMe provided.  My top “bad news” item is indeed the same item that is reported at 23andMe.  Having said that, there are a lot more and different items here that were not reported at 23andMe.  After looking at the varied results from Promethease, I suspect that 23andMe was trying to distill data on my behalf.

However, Promethease does not attempt to analyze your results.  Some mutations are known to be connected to multiple conditions, so they simply tell you that.  In some cases, you will have some negative and some positive mutations for the same disease.  Again, they simply inform you, complete with a reference.  It’s worth noting that for one disease I’m particularly interested in, Parkinson’s, I have a lot of conflicting data, pages worth.  This just goes to show how complex interpreting this information really is, and shows that genetic predisposition, positive or negative, with only a few exceptions, is not genetic predetermination.

My good news made me feel really good.  I’m at decreased risk of frontotemporal dementia or Alzheimer’s and Parkinson’s.  I’m optimistic and empathetic.  I wonder if this has anything to do with selecting the bad news option first – I knew I had the good news to look forward to.  Get the bad stuff over with and get on with it…

Ironically, some of my good news items are in direct conflict with some of my bad news items.  And yes, some are Parkinson’s, which has apparently been more heavily studied that some other diseases.  Hopefully, the decreased and elevated risks will cancel each other out and I’ll just be average.

However, when running my Ancestry data file at Promethease, one of my elevated risks was Parkinson’s, based on the SNPs discovered in the 23andMe research, which conflicts directly with the information provided based on the 23andMe raw data file.  Searching further, different SNPs have been reported to either be associated with increased or decreased incidence of the disease – and I carry some of each – but none are extremely elevated.

So where does this leave me in terms of whether Mom had Parkinson’s, or not?  There is nothing to indicate an extremely high risk of Parkinson’s.  Some indicators are for elevated risk, some for reduced risk.  Compared to the one condition I know she had, which has a very highly elevated risk in all 3 reports, the Parkinson’s risk is simply unremarkable and doesn’t stand out.  Bottom line – I still don’t know for sure, but I still don’t think she had Parkinson’s.  Had I found highly elevated risk factors,  I would have rethought my opinion.

Many diseases have multiple genetic components along with other external factors.  Of course, not all studies report the same findings, and this report is based on academic medical studies.

Rarely are genetic predispositions more than just that, a slightly increased or decreased probability.  Few are fatal and some are more of a life sentence than a death sentence.  Having said this, there are notable exceptions, and if you really don’t want to know a worst case scenario, or aren’t prepared to deal with the results, don’t participate in DNA testing or reporting for medical or health information.  If you have reason to suspect your family may carry one of the genetic terminal illnesses, visit your doctor for advice.

And speaking of physicians, much of this information, such as the information about how certain medications are metabolized could be critically important.  In my case, I’m actually taking one of the mediations that is referenced where I have a decreased sensitivity.  Yep, I knew that, but now I can provide this information to my physician.

For those who tend to worry and borrow trouble they don’t yet have, running this type of report might not be a good idea.  It’s certainly not for hypochondriacs – IMHO.  It’s a personal choice, and a very inexpensive one at that, so financially available to everyone.  If what it contains is going to worry you, don’t do it.  I noticed that there are several anxiety categories in these reports – but then you have to run the report to see if you carry them – kind of a catch 22 if you tend to be anxious and worry.

My personal perspective is that there may be information here that is valuable to me, or to my physicians, or to my children.  The worst “bad news” item I already knew about through 23andMe, but I also anticipated that condition, without genetic testing, because my mother had this same disease in old age.  I’m not referring now to the Parkinson’s, but a vision related condition that she definitely did have.  This item was also consistently reported at a high degree of risk utilizing the data files of 23andMe, Family Tree DNA and Ancestry.  Thankfully, it is an old age problem and one that can be treated, if not cured today.  The Promethease reports, along with 23andMe’s report, have simply reinforced that I need to be proactive and vigilant and to eat lots of veggies.  The good news is that many items include preventative measures in the verbiage or associated studies that your Promethease report links to at SNPedia.

How does this report compare to the 23andMe experience, assuming 23andMe was still an option or might be again in the future for health information?  The 23andMe customer interface is much smoother and more user friendly.  It seems to be focused on more “fun” and less “worry.”  The Promethease report is that, a report, although they do a great job making it interactive.  There is no sugar coating – just the facts Ma’am.  And I think it’s actually much easier to use.  You can easily search by disease, by category, and the searches actually work.

Promethease differs in another way too.  Personally I like the idea that my data is mine, I’m in complete control of it, and it’s not being sold by Promethease out the back door for studies or purposes I might not be too thrilled about.  I don’t want my DNA to be used to patent genes that cause the tests for the condition to be restricted to the patentee at dramatically inflated prices.  While the Supreme Court determined that genes can’t be patented in the case of the BRCA breast cancer genes, the fight continues with lawsuits being filed, and 23andMe holds a Parkinson’s patent that was obtained by utilizing customer data.   Nor do I want my data to be used to patent the technology for “designer babies.”  If my DNA is going to be utilized for research, I want the ability to authorize that use, specifically.

Therefore, I feel much better about uploading a raw data file from an autosomal test at a firm like Family Tree DNA, who NEVER sells or otherwise divulges my data without first requesting permission.  I thereby maintain complete control over my genetic results, rather than utilizing companies who either sell (or otherwise utilize) my results or reserve the right to do so.  This is the case with both 23andMe and Ancestry.com, and to be clear, they have never claimed otherwise.?????????????????????????????

And oh, I forgot to mention…I am just so relieved….I have a decreased risk of baldness….

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.

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

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

http://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.

http://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/

http://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/

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

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

http://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.

http://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/

http://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.

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

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

http://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.

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

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

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

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

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

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

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

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

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

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

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

http://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.

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

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

http://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.

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

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

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

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

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

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

http://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

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

http://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.

http://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.

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

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

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

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

http://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.

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

http://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

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

http://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.

http://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

http://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….

Free Webinars from Family Tree DNA

Recently, one of my cousins told me that she was utterly mystified by her results at Family Tree DNA.  I could tell that she was confused between Y line testing and autosomal testing and what each of them could, would or might do for her.  Because she was confused, she saw no value in testing.  Ouch!

These conversations distress me, greatly, especially when people don’t understand the value they do receive – because they tell other people.  I know that if people really do understand how to utilize these tools, they will only have good things to say about genetic genealogy and testing.  It has broken down so many walls for so many people.  Ironically, it’s how I found that cousin.

Genetic genealogy is a word of mouth field – and the more people who test and participate in the various data bases – the more answers will be found by all of us.

Given this, I am particularly pleased to see that Family Tree DNA has teamed up with Elise Friedman, of Relative Roots, to offer free educational webinars focused on the basics of genetic genealogy and how to understand and use your results.

The live webinars will be recorded and uploaded to any-time format after the live sessions.  I don’t know how long these will be available (in the past, about a month,) so if you are interested, do watch them now.  The first live session took place last week, and it’s available now as a recording.

I also understand that Family Tree DNA will be offering monthly educational Webinars, so stay tuned for more.

*Introduction to Family Tree DNA*

Any Time Recording

Registration: http://bit.ly/1cGd447

FTDNA webinar

This FREE Online Seminar will help you learn the basics about Family Tree DNA’s Y-DNA, mtDNA and Family Finder (autosomal DNA) tests. Elise explains what each of these tests can tell you about your ancestry and how to decide which test to order based on your personal interests and goals. She shows the basics of personal myFTDNA account where all of your results are reported as well as example results from each test. Elise will also gives a brief overview of our group projects and other resources available at Family Tree DNA.

*Family Tree DNA Results Explained, Part 1: Y-DNA*

(Live) Thursday, 12/19/2013, 12pm Central (10am Pacific, 11am Mountain, 1pm  Eastern, 6pm GMT)

Registration: http://bit.ly/JCF4vn

FTDNA webinar 2

In this information-packed webinar, Elise focuses on how to read and understand your Y-DNA results. Learn where to find your Y-DNA results in your personal myFTDNA account, how to read your Standard Y-STR Results and what they mean, how to analyze your Y-DNA matches, what your Y-DNA haplogroup means and much more. She also provides tips for making the most of your Family Tree DNA experience

*Family Tree DNA Results Explained, Part 2: mtDNA*

(Live) Monday, 12/23/2013, 12pm Central (10am Pacific, 11am Mountain, 1pm Eastern, 6pm GMT)

Registration: http://bit.ly/1kcnRqk

ftdna webinar 3

In this webinar, Elise focuses on how to read and understand your mtDNA results. Learn where to find your mtDNA results in your personal myFTDNA account, how to read your mtDNA Results page and what the results mean, how to analyze your mtDNA matches, what your mtDNA haplogroup means and much more.  She also provides tips for making the most of your Family Tree DNA experience.

Family Tree DNA’s Family Finder Match Matrix Released

Wow, today is a great day in genetic genealogy-land.  After the conference in Houston, which ended just a month ago today, a small group met with the Family Tree DNA team and explained what we, as users, need, and why.  We walked through lots of scenarios and everyone did a lot of explaining.  The whiteboard was full.  We were hopeful.

Bennett made a commitment, publicly, at the conference, to do whatever it took.  However, I never expected this feature, the Family Finder Match Matrix, which was very high on the priority list, to make it out the door this soon.  Less than one month later.  Hats off to the Family Tree DNA team!  YOU ROCK!!!

Why is this so important?  Because you have two halves to your chromosome, and there is no magic zipper to divide Mom’s half from Dad’s half.  So you’re going to match with people who come from Mom’s side, Dad’s side, and some who just happen to match because of random recombination.  The best way to figure this out is to see which of your matches match each other as well.

So, in a nutshell, here’s how this works.

  • If your matches match you, but not your other matches as revealed in the “In Common With” feature, they are questionable matches.  To find who you match in common with one of your matches, use this crossover icon on your matches page:

ftdna 12-4

  • If your matches match you and each other, then they are very likely important genealogical matches.
  • If your matches match you and each other, and you can identify the lineage based on which of your cousins or other family members they match, you’ve got a hugely valuable piece of information.  I discussed this in yesterday’s article, Chromosome Mapping aka Ancestor Mapping.

Here’s the release today from Family Tree DNA.  And even better news, they have promised to keep us apprised on new features to come ON A WEEKLY BASIS!!!

From Family Tree DNA:

Today, we are happy to release our new BETA Family Finder – Matrix page. The Matrix tool can tell you if two or more of your matches match each other. This is most useful when you discover matches with wholly or partly overlapping DNA segments on the Family Finder – Chromosome Browser page.

Due to privacy concerns, the suggested relationship of your two matches (if related) is not revealed. However, we can tell you whether they are related according to our Family Finder program. To use it, you select up to 10 names from the Match list on the left side of the page and add them to the Selected Matches list on the right side of the page. A grid will populate below the lists. It will indicate whether there is a match (a blue check mark) or there is not a match (an empty white tile).

You access the BETA Family Finder – Matrix page through the Family Finder menu in your myFTDNA account.

matrix 1

The page starts out with two list areas: Matches and Selected Matches. You add Matches to the Selected Matches list by clicking on a name and then on the Add button.

matrix 2

Here is a screenshot of the BETA Family Finder – Matches page with a few matches added to the Selected Matches list.

matrix 3

You can change the order of names in the matrix by clicking on a name and then either the Move Up or the Move Down button.

Matrix 4

To remove someone from the Selected Matches list, click on their name and then the Remove button.