Ancestry Kit Mixup

Every genealogists worst nightmare.  A DNA kit swap.  You unknowingly receive the results from someone else, and that equally in-the-dark unknown person receives yours.  And you’ll never know unless you recognize the signs and take action to see if it’s your bad luck or overactive imagination, or the answer really is a kit swap or lab error of some sort.

I’ve just spent three months unraveling this exact situation that occurred at Ancestry.com.  The person to whom this happened would like to share her story with you.  We are hoping that if something similar ever happens to you, that you’ll be able to recognize the signs and know what steps to take to figure out if this indeed has occurred.

Let me also say that a kit swap or similar lab error is really quite rare, and in most other instances when people believe their kits have been swapped, they haven’t been, although this certainly is not the first time this has happened.  CeCe Moore reported on another Ancestry.com case in 2012.

We’ll call the lady Jane. Jane’s father agreed to have his Y DNA tested some years ago at Ancestry.com.  Jane submitted his DNA for him and noticed that he had no matches to his rather common surname.  She didn’t really think anything of it at the time, other than being disappointed.  His haplogroup was estimated by Ancestry to be R1b.

As time went on, she ordered Ancestry.com’s autosomal test too for her father.  Ancestry sent another sampling kit, and her father is receiving matches to people who, at least according to their trees, share common ancestors with her father.

Last year, Jane decided to transfer her father’s Y DNA to Family Tree DNA. The markers from Ancestry.com were transferred, and Jane still didn’t have any surname matches at Family Tree DNA.

Jane then ordered the Geno2.0 test for her father.  The results were returned with haplogroup I, terminal SNP I-L22, which were at odds with Ancestry’s haplogroup R1b estimate.

About the same time, Jane upgraded her father’s STR markers as well, and the haplogroup project administrator noticed that while Jane’s father’s lower panels, meaning the ones tested at Ancestry matched haplogroup R1b, his upper panels didn’t match R1b subgroups at all.

Obviously something was wrong, very wrong, someplace.  But what, and where?  Jane contacted me and asked if I would help unravel this puzzle.

I checked Jane’s father’s page at Family Tree DNA, and when she transferred his Geno 2.0 results to his FTDNA page, apparently the transfer confused the software at FTDNA because his results reported both I-L22 and R-M269 as positive, which is impossible since I-L22 is in haplogroup I, only, and R-M269 is only found in haplogroup R.

ancestry kit swap ftdna snps

Unfortunately, this only added to the confusion.

At this point, I downloaded the raw data file from the Geno 2.0 test and verified that indeed, M269 was absent and L22 was present.

ancestry kit swap raw data

Family Tree DNA, thankfully, stepped up to the plate and ran a SNP test on Jane’s father’s second vial.  That SNP test also came back as positive for haplogroup I, matching the Geno 2.0 results.

Just to be absolutely positive, Family Tree DNA sent Jane’s father a third vial and tested the same markers that Jane had transferred from Ancestry.  You can see for yourself – the results are very different.  The results are unquestionable.  Either there was a kit swap or a lab error of some sort at Ancestry where the wrong markers were posted for Jane’s father’s results.  He has been tested three times, from separate vials, at Family Tree DNA with all of the results providing evidence that the Ancestry results were in error.

Marker Ancestry FTDNA
DYS438 12 10
DYS391 10 11
DYS392 13 11
DYS426 12 11
DYS439 13 11
DYS445 12 11
GGAAT1B07 10 11
DYS444 11 12
DYS446 13 13
DYS462 11 13
Y-GATA-A10 13 13
DYS437 15 16
DYS441 14 16
DYS458 17 16
DYS463 24 21
DYS635 23 21
DYS452 30 31

In an overabundance of caution, Family Tree DNA is going to rerun the entire test, all markers and the backbone SNP, from yet another (fourth) new vial being sent to Jane’s father.  Thank heavens Jane’s father is still available for testing and not entirely discouraged.

Jane is ecstatic, because now, she is actually receiving surname matches and in her father’s words, “we just wanted to know who we are.”  And just in time for Father’s Day!

Signs and Signals

How might you know if a kit swap has happened to you?  As we know, Ancestry has discontinued their Y and mitochondrial DNA testing and will be destroying the data base, so this won’t be an issue at Ancestry with new Y DNA kits, but it could be an issue for results already delivered, like Jane’s, and for autosomal tests.  This is one reason why retesting might not be a bad idea, even though the $19 or $58 Y DNA Ancestry to FTDNA transfer price is quite attractive.  Here are some of the signs that might tip you that there is a problem:

  1. If Y DNA, you don’t receive any surname matches, even to those you believe that you are in related to. This is one of those sticky-wickets, because if you don’t match your first cousin, for example, the most likely situation is that you have an undocumented adoption in one of the lines. My suggestion in this situation is to submit an entirely new test under a new kit number. If your first and second kits match each other, then the answer is the undocumented adoption.
  2. If autosomal DNA, and you have no matches to anyone you believe you should match, especially close relatives, submit your DNA to one of the other three testing companies – Family Tree DNA, 23andMe or Ancestry.com. The approach gives you the benefit of fishing in multiple ponds along with verifying that your results match each other. When you receive the results from both companies, download the raw data files from both to www.gedmatch.com and then match them to each other. They should match almost exactly, although there will be some small differences in terms of areas tested and possibly no-calls – but they should match very closely.

Let’s hope this never happens to anyone else.  The sad thing is that whoever, at Ancestry, received Jane’s father’s Y DNA results likely has no idea they are incorrect.

Thank you Family Tree DNA for going above and beyond to resolve this very distressing situation for Jane and her father.

Family Tree DNA Surpasses the Million Test Mark

Family-Tree-DNA logo

Family Tree DNA, the genetic genealogy arm of Gene by Gene, announced today in a press release that it has processed over 1,000,000 DNA test kits results for genealogy and anthropology purposes.

This historic amount includes Family Tree DNA’s tests as well the processing of public participation samples for National Geographic’s Genographic Projects genetic testing partner.

The million-test milestone was reached this week during the company’s Father’s Day sale, which includes the Family Finder test currently discounted to the price of $79 and the Big Y at $595.  So if you purchased one of these tests this week, you could have been that historic millionth person!

The press release goes on to say:

Family Tree DNA offers the widest range of DNA testing services in the field of genetic genealogy.  The company prides itself on its commitment to the practice of solid, ethical science. Family Tree DNA has the largest database in the world for matching purposes, which means increased chances of finding long lost relatives. In that regard, Family Tree DNA is an important resource for the three million people in the United States who either were adopted or descend from adoptees.

Founded in 2000, Gene By Gene, Ltd. is a CAP-accredited and CLIA-registered genetic testing company that serves consumers, researchers, and physicians. Gene by Gene offers a wide range of regulated clinical diagnostic tests, as well as research use only (RUO) tests. The Family Tree DNA division of Gene by Gene is a pioneer and leader in DNA testing for genealogy and ancestry. The company operates the largest genetic genealogy database in the world and has provided more than 5 million discrete genetic tests.

It seems like only yesterday that I ordered kit 6656, but it was December of 2002, nearly a dozen years ago.  On New Year’s Eve of 2005, right at midnight, I ordered kit 50,000.  The genetic genealogy community was very excited at that milestone as well.  Eight and a half years later, one million.  It took Family Tree DNA 3 years, from 2002 to 2005, to sell 43,000 kits, or about 14,500 kits per year.  Between 2005 and today, they have sold another 950,000 kits, or just over 100,000 per year, on average.

The 5 million number also suggests that the average client has purchased 5 different tests or upgrades, per kit.  In my case, that’s true because I began purchasing when only the HVR region of mtDNA was available, so I’ve upgraded several times and purchased every test or upgrade Family Tree DNA has ever offered.  All in the unquenchable thirst to learn more about my ancestors.

Congratulations Family Tree DNA on this historic and important milestone.  May your second million happen quickly and include a lot of my relatives:)

Big Y and Family Finder Sale, Plus $100 Coupon for Big Y

Family Tree DNA almost always has a Father’s Day sale, and they have just announced this year’s sale.  It’s a good one, especially if combined with a separate special $100 coupon for the Big Y test.

father day sale 2014

Right now, the Father’s Day Sale provides the Family Finder (autosomal) test for $79.  This test is available for everyone to take and provides you with cousin matches from all of your genealogical lines, plus ethnicity estimates.  This is the lowest price I’ve ever seen for this test, or this type of test, at any vendor.

Even more remarkable, is that you’ll be able to purchase the Big Y, not for the $595 listed above, but if you use the special coupon code listed below, you’ll be able to save another $100 and purchase the Big Y for an amazing $495.  The Big Y is an advanced Y DNA test for those clients who have already purchased STR marker testing.

Furthermore, by the time you receive those Bit Y results, the new SNP matching will be in place so you’ll be able to easily see who you match.  Now is the time to begin testing those various family groups to see if there are family-line defining SNPs within groups who match closely on STR markers.

All I can say is WooHoo – brick walls are gonna fall……

Oh, the coupon code – you want the special $100 off coupon code – pardon my excitement – here it is…..FDS140997

Click here to order.

Thank you Family Tree DNA and by the way, Happy Father’s Day!!!

PS – The code above is the code I received because I had previously purchased a Big Y test.  First come, first served.  It can only be utilized once.  If mine has been used, you might contact your project admin to see if there are extra ones within your projects.  Conversely, anyone who has any extra code feel free to post it in the comments.

Bennett Greenspan – The Future of Genetic Genealogy

Bennett SCGA 2014 v2

Bennett Greenspan, one of the founders of Family Tree DNA, spoke about “The Future of Genetic Genealogy” at the Southern California Genealogy Society conference this week.  The SCGS has been gracious enough to provide a video of the livestream.

High points of Bennett’s presentation include:

  1. There will be a new Y SNP matching capability released in the next few days.
  2. “Regulatory issues are larger issues than the science.” Bennett discusses “armwrestling with the FDA.”
  3. If prices of SNP chips that test over 2 million locations don’t drop substantially in the next couple of years, then genealogy testing likely will not utilize the next generation of SNP chip, but will move directly to full genome sequence testing. This may happen in the 3-5 year range but will, for sure in the 5-10 year range.

Bennett talked quite a bit about privacy and what privacy is in this technology era, expectations and how privacy expectations may affect future DNA testing.  Be sure to watch the video. It’s always interesting to hear Bennett, functionally the father of genetic genealogy, speak about this industry and the future.

Ancestry.com Discontinues Y and mtDNA Tests and Closes Data Base

ancestry to ftdna

Ancestry.com has not been actively selling Y and mtDNA tests for some time now.  However, today Ancestry announced the official discontinuance of those tests and that as of September 5th, their Y and mtDNA data bases will also be shuttered – meaning that the results will no longer be accessible for those who tested or for anyone wanting to do a comparison.

This is very sad news indeed for the genetic genealogy community, especially given that Ancestry has in the past purchased other vendors such as Relative Genetics and incorporated their results into their data base.

For anyone who tested their Y DNA with Ancestry, now is the time to transfer those result to the Family Tree DNA data base, now the last vendor left standing who provides those tests along with a comparison data base.  This is easy to do and you can be a part of the Family Tree DNA community, availing yourself of their surname projects for only $19.

If you want to see your matches, you can upgrade your kit from Ancestry’s 33 or 46 markers to Family Tree DNA’s standard markers for another $39 at the same time you transfer your Ancestry results.  This also has the added benefit of having your actual DNA in the lab at Family Tree DNA where it will be archived for 25 years.  I’m already hearing moans from people whose family DNA is only at Ancestry, and the original tester has passed away.

In fact, if you don’t transfer your results from Ancestry now, or before September 5th, you will lose your opportunity as your Y and mtDNA results will no longer be available at Ancestry in any format, according to their FAQ.

Ancestry states that this change does not affect their autosomal DNA testing, and in fact, that’s where they want to focus, at least for now.  Unfortunately, the shuttering of their Y and mtDNA data bases calls into question their commitment to the genetics aspect of the genealogy industry.  Autosomal DNA testing will be a priority as long as it’s profitable, just like Y and mtDNA has turned out to be.

I would suggest while you are transferring, you might also want to take advantage of this opportunity to also transfer your Ancestry autosomal results to Family Tree DNA for $69.  You can fish in a second match pool and Family Tree DNA offers many tools to participants that Ancestry does not offer.

If you’re not inclined to transfer your results to Family Tree DNA, at least avail yourself of the two free data bases, www.ysearch.org for Y results and www.mitosearch.org for mtDNA.  At least your results won’t be entirely lost forever.

I understand that Ancestry doesn’t want to sell the Y and mtDNA products any longer, but I would think that maintaining the current Y and mtDNA data bases in a static state for the tens of thousands of people who have spent a nontrivial amount of money DNA testing, and allowing comparisons, would be well worthwhile in terms of customer loyalty if nothing else.  Customers are viewing this move as abandonment and a betrayal of their trust, and it begs the question of what will eventually happen to autosomal results and matches at Ancestry.  If you’re going to test at Ancestry, make sure you also test at Family Tree DNA so your actual DNA is available there as well.

Native American DNA Projects

Native DNA in Feathers

I’m often asked about projects that are for or include Native American DNA results.  Please note that different project administrators have different criteria for admission to a project.  Some require definitive proof of descent, some require no documentation at all.  This is entirely left to the discretion of the project administrators.  Therefore, you should NEVER assume that because you match someone in one of these projects that you have Native heritage.  There are various ways to prove Native heritage using DNA which I’ve discussed in the article, “Proving Native American Ancestry Using DNA.”

Furthermore, some of these projects aren’t exclusively for Native American descendants, but you may find Native descendants or families among the project members because of the topic or where the project is focused.

Regarding haplogroup projects.  Some haplogroups include both people who are and who are not Native.  Check with the particular project to understand the nuances.  In many cases, research through the projects is ongoing.

If you know of additional projects which should be added to this list, please let me know.

Native American, First Nations or Aboriginal DNA Projects

Acadia Metis Mothers
http://www.familytreedna.com/public/AcadiaMetisMothers/default.aspx

Algonquian East DNA Project
http://www.familytreedna.com/public/algonquian_east/default.aspx

American Indian DNA Project
http://www.familytreedna.com/public/AmericanIndian/

AmerIndian Ancestry out of Acadia Project
http://www.familytreedna.com/public/AcadianAmerIndian/

Cherokee DNA Project
http://www.familytreedna.com/public/CherokeeDNAProject/default.aspx

Lumbee Tribe Regional DNA Project
http://www.familytreedna.com/public/LumbeeTribe/

Mexico and Southwest USA Native Y
http://www.familytreedna.com/public/MexicoAmerindian/

Mitochondrial American Indian Founder Project
http://www.familytreedna.com/public/AmerindFoundermtDNA/default.aspx

Mothers of Acadian mtDNA Project
http://www.familytreedna.com/public/mothersofacadia/default.aspx

Native People of Southwest Virginia
http://www.familytreedna.com/public/napeopleofswvirginia/

North Carolina Native Heritage Project
http://www.familytreedna.com/public/NorthCarolinaNativeHeritage

Piqua/Shawnee – no public website – contact admins below
cavetank@aol.com, tankerkh@uc.edu, ewest14@woh.rr.com

Tuscarora
http://www.familytreedna.com/public/Tuscarora/

Waccamaw DNA Project
http://www.familytreedna.com/public/CapefearIndians/default.aspx

Wesorts-Piscataway
http://www.familytreedna.com/public/Wesorts-Piscataway

Wiccocomico Native American DNA Project
http://www.familytreedna.com/public/wiccocomico/default.aspx

Mitochondrial DNA Haplogroup Projects

Haplogroup A Mitochondrial DNA
http://www.familytreedna.com/public/haplogroupAmtDNA/
Note – Native American DNA is a subgroup of haplogroup A.  See this link for specifics.

A2 Mitochondrial DNA Project
http://www.familytreedna.com/public/mtDNA_A2
A2 is known to be Native.

A4 Mitochondrial DNA Project
http://www.familytreedna.com/public/A4-mtDNA/
Haplogroup A4 is known to be Native.

B2 Mitochondrial DNA Project
http://www.familytreedna.com/public/mt-DNA-B/
B2 is known to be Native.

Haplogroup C Mitochondrial DNA Project
http://www.familytreedna.com/public/C_Haplogroup_mtDNA
Subgroups of haplogroup C are known to be Native.

Haplogroup D Mitochondrial DNA Project
http://www.familytreedna.com/public/D/
Subgroups of haplogroup D are known to be Native.

Haplogroup X Mitochondrial DNA Project
http://www.familytreedna.com/public/x/
Subgroups of haplogroup X are known to be Native.

Haplogroup X2b4 Mitochondrial DNA Project
http://familytreedna.com/public/x2b4mtdna
X2b4 is currently being studied to determine if it is Native or has a Native component.

Y Haplogroup Projects

Y Haplogroup C
http://www.familytreedna.com/public/Chaplogroup/
Subgroups of haplogroup C are known to be Native.

Haplogroup C-P39
http://www.familytreedna.com/public/ydna_C-P39/#sthash.cKkws2cd.dpbs
This SNP defined Native Americans within haplogroup C.

Haplogroup Q Project
http://www.familytreedna.com/public/yDNA_Q/
Subgroups of haplogroup Q are known to be Native.

American Indian Haplogroup Q1a3a1 – QM3
http://www.familytreedna.com/public/Amerind%20Y/?/publicwebsite.aspx?vgroup=Amerind+Y

Related Topics

You may find Native families listed in these projects.

Cumberland Gap Mitochondrial DNA Project
http://www.familytreedna.com/public/Cumberlandgap-mtdna/?/publicwebsite.aspx?vgroup=Cumberlandgap-mtdna

Cumberland Gap Y DNA Project
http://www.familytreedna.com/public/CumberlandGap-YDNA

Early Chesapeake
http://www.familytreedna.com/public/Early_Chesapeake

East Carolina Roots
http://www.familytreedna.com/public/eastcarolinaroots/default.aspx

Melungeon Core Y Project
http://www.familytreedna.com/public/coremelungeon

Melungeon Mitochondrial DNA
http://www.familytreedna.com/public/melungeonmtdna/

Melungeon Families
http://www.familytreedna.com/public/familiesofinterest

Mitochondrial DNA of the Middle Appalachians
http://www.familytreedna.com/public/mtDNA%20of%20Middle%20Appalachians/default.aspx?section=mtresults

New Mexico DNA Project
http://www.familytreedna.com/public/newmexicoDNA/

North Carolina Early 1700s
http://www.familytreedna.com/public/NorthCarolinaEarly1700s/default.aspx

Puerto Rico DNA Project
http://www.familytreedna.com/public/puertoricansurname/

Southwestern Virginia Roots
http://www.familytreedna.com/public/SWVirginia

Virginia 1600s
http://www.familytreedna.com/public/va-1600s

Voices in Time
http://www.familytreedna.com/public/voicesintime/

Finding Native American Ethnic Results in Germanic People

I’m often asked about the significance of small percentages of autosomal DNA in results.  Specifically, the small percentages are often of Native American or results that would suggest Native admixture.  One of the first questions I always ask is whether or not the individual has Germanic or eastern European admixture.

Why?

Take a look at this map of the Invasion of the Roman Empire.  See the Huns and their path?

Hun map

It’s no wonder we’re so admixed.

Here’s a map of the Hunnic empire at its peak under Attila between the years 420-469.

Hun emplire

But that wasn’t the end of the Asian invasions.  The Magyars, who settled in Hungary arrived from Asia as well, in the 800s and 900s, as shown on this map from LaSalle University.

magyar map

Since both the Hungarians and some Germanic people descend from Asian populations, as do Native Americans, albeit thousands of years apart, it’s not unrealistic to expect that, as populations, they share a genetic connection.

Therefore, when people who carry heritage from this region of the world show small amounts of Native or Asian origin, I’m not surprised.  However, for Americans, trying to sort out their Native ethnic heritage, this is most unhelpful.

Let’s take a look at the perfect example candidate.  This man is exactly half Hungarian and half German.  Let’s see what his DNA results say, relative to any Asian or Native heritage, utilizing the testing companies and the free admixture tools at www.gedmatch.com.

He has not tested at Ancestry, but at Family Tree DNA, his myOrigins report 96% European, 4% Middle Eastern.  At 23andMe in speculative view, he shows 99.7 European and .2 sub-saharan African.

Moving to the admixture tools at GedMatch, MDLP is not recommended for Asian or Native ancestry, so I have excluded that tool.

Eurogenes K13 is the most recently updated admixture tool, so let’s take a look at that one first.

Eurogenes K13

 JK Eurogenes K13 v2

Eurogenes K13 showed 7% West Asian, which makes perfect sense considering his heritage, but it might be counted as “Native” in other circumstances, although I would certainly be very skeptical about counting it as such.

However, East Asian, Siberian and Amerindian would all be amalgamated into the Native American category, for a combined percentage of 1.31.

jk eurogenes k13 chart

However, selecting the “admixture proportions by chromosome” view shows something a bit different.  The cumulative percentages, by chromosome equate to 10.10%.  Some researchers mistakenly add this amount and use that as their percentage of Native ancestry.  This is not the case, because those are the portions of 100% of each individual chromosome, and the total would need to be divided by 22 to obtain the average value across all chromosomes.  The total is irrelevant, and the average may not reflect how the developer determines the amount of admixture because chromosomes are not the same size nor carry the same number of SNPs.  Questions relative to the functional underpinnings of each tool should be addressed to the developers.

Dodecad

I understand that there is a newer version of Dodecad, but that it has not been submitted to GedMatch for inclusion, per a discussion with GedMatch.  I can’t tell which of the Dodecad versions on GedMatch is the most current, so I ran the results utilizing both v3 and 12b.

jk dodecad v3

jk dodecad v3 chart

I hope v3 is not the most current, because it does not include any Native American category or pseudocategory – although there is a smattering of Northeast Asian at .27% and Southwest Asian at 1%.

Dodecad 12b below

jk dodecad 12b

The 12b version does show .52% Siberian and 2.6% Southwest Asian, although I’m not at all sure the Southwest Asian should be included.

HarappaWorld

jk harappaworld

jk harappaworld chart

Harappaworld shows .09 Siberian, .27% American (Native American), .23% Beringian and 1.8% Southwest Asian, although I would not include Southwest Asian in the Native calculation.

In Summary

Neither Family Tree DNA nor 23andMe find Native ancestry in our German/Hungarian tester, but all 3 of the admixture tools at Gedmatch find either small amounts of Native or Asian ancestry that could certainly be interpreted as Native, such as Siberian or Beringian.

Does this mean this German/Hungarian man has Native American ancestry?  Of course not, but it does probably mean that the Native population and his ancestral populations did share some genes from the same gene pool thousands of years ago.

While you might think this is improbable, or impossible, consider for a minute that every person outside of Africa today carries some percentage of Neanderthal DNA, and all Europeans also carry Denisovan DNA.  Our DNA does indeed have staying power over the millennia, especially once an entire population or group of people is involved.  We’ve recently seen this same type of scenarios in the full genome sequencing of a 24,000 year old Siberian male skeleton.

Our German/Hungarian man carries 2.4% Neanderthal DNA according to 23andMe and 2.7% according to the Genographic Project, which also reports that he carries 3.9% Denisovan.  The European average is about 2% for Neanderthal.

The net-net of this is that minority admixture is not always what it seems to be, especially when utilizing autosomal DNA to detect small amounts of Native American admixture.  The big picture needs to be taken into consideration.  Caution is advised.

When searching for Native admixture, when possible, both Y DNA and mitochondrial DNA give specific answers for specific pedigree lines relative to ancestry.  Of course, to utilize Y or mtDNA, the tester must descend from the Native ancestor either directly paternally to test the male Y chromosome, or directly matrilineally to test the mitochondrial line.  You can read about this type of testing, and how it works, in my article, Proving Native American Ancestry Using DNA.  You can also read about other ways to prove Native ancestry using autosomal DNA, including how to unravel which pedigree line the Native ancestry descends from, utilizing admixture tools, in the article, “The Autosomal Me.”