Hackers and Your Genetic Secrets

Posted on January 20, 2013 by Roberta Estes

Did that title get your attention? Well, it was meant to, just like it was meant to in this NBC article titled “Scientists Demonstrate How Hackers Could Unlock Your Genetic Secrets.” Or how about this one in the New York Times, “Web Hunt for DNA Sequences Leaves Privacy Compromised?” Sensationalism sells….and so does fear. Don’t panic, the sky is not falling.

I’ve had several people forward me a variety of links to several articles about this expressing concern. Most people didn’t really understand what was going on…and since “family tree databases” were mentioned in the first paragraph, it frightened them.

This article says that the “security cracking trick relies on the availability of genetic information linked to surnames in a variety of public family-tree databases.” Well, that’s sort of true, but not exactly true. The issue is not the family tree databases, it’s the fact that the researchers in The Thousand Genomes Project, while keeping the names of those 1000 people “anonymous,” provided enough information that these scientific researchers, not hackers, were able to data mine the 1000 Genomes participants information to determine their Y-DNA marker values, then compared those haplotypes (marker values) just like we do in databases such as Ysearch and Sorenson. And yes, they likely had matches to several surnames, like most of us do.

Individuals in the 1000 Genomes Project signed a release indicating that they knew that their data was to be used publicly, although their identity would not be revealed but that researchers could not guarantee their privacy. The 1000 Genomes Project, unfortunately, posted the ages of the participants, which at the time seemed innocuous enough, and it was common knowledge within the scientific community that they all lived in Utah. With these three pieces of information, their age, their location, and from the scientists data mining, a possible surname, the scientists were then able, if the surname wasn’t something like Smith or Jones, to use publicly available Google and “white pages” types of searches to find people in that state, of that age, by that surname, and then using obituaries and such, connect them through online family trees to their more distant families. They did this with Craig Venter, for example.

This technique is nothing new to genealogists, as we’ve been finding cousins that way for years – the difference being of course that we didn’t data mine, otherwise in this case more aptly referred to as “scientific hacking,” the 1000 Genomes Project in order to find their Y-line DNA markers to determine a possible surname for them. That is the issue and the point of this article and ironically, it’s scientists who did it, then published the “how-to” manual.

Any genetic genealogist knows, especially anyone dealing with adoptees, that you can only reveal a biological surname about 30% of the time. In fact the scientists success rate was lower, 12%. But that’s actually irrelevant in the bigger context of the article. Their point was that they succeeded at all.

This is sort of like putting personal information on the internet, except your name, and then being surprised that someone could connect the dots and put the pieces together. No one would be surprised today if that were to happen. In fact, I’m sure we all have received cautions and warnings about putting too much info on Facebook because burglars were robbing homes when people were vacationing. Many people have their hometown, their high school and their birthday and year publicly available on Facebook. Now how many “security questions” does that answer right there? Combine that with your dog’s name and your mother’s maiden name and you’ve got almost all of the common ones.

Aside from the fear-mongering, I have three issues with these reports as a whole.

1. Statements like “they traced those three family tree pedigrees to find other connections between relatives and sensitive genetic data.” Whoa, stop right there. Just because you share a surname or even if you are a direct and immediate relative, that says nothing, absolutely nothing, about whether or not you inherited some genetically disposed health issue. Remember, children inherit half of their DNA from each parent. So unless they are finding identical twins or parents, one cannot infer that an entire family tree of people share frightening health traits. It’s irresponsible to suggest otherwise.

2. “For years, experts have worried that sensitive genetic data could be used to discriminate against patients, potential employees or would-be insurance customers. Such discrimination is illegal when it comes to employment or health insurance, but the law doesn’t’ cover life insurance, disability insurance or long-term care insurance. Theoretically an insurer could search through genetic records and turn you down because you have a genetic predisposition to, say, Alzheimer’s disease.”

Discrimination is an issue, and laws have been put in place to prohibit discrimination in the workplace. But insurers aren’t going to sift through genetic data like a private investigator. Suggesting this is unnecessary fear-mongering. Insurers don’t do that, they simply tell you that a blood test is a pre-requisite of obtaining insurance. I know, I bought life insurance and they sent a nurse to my house to verify my identity and take a blood sample. At that time, they were looking for diabetes, AIDs and probably a whole lot more. Today, they might be looking for genetic pre-dispositions. I don’t know, but I do know they have a direct method of obtaining that information and it’s not spending untold hours sifting through someone else’s data that likely isn’t relevant to you anyway.

3. This “research” project was inspired at Whitehead Institute, an affiliate of MIT, a publicly funded institution. When Yaniv Erlich dreamed up this new hacking technique, he said he couldn’t resist trying it, so instead of simply discovering a potential issue and privately and quietly working with the proper people to resolve the issue, he decided to exploit it publicly, obtaining, I suppose, his 15 minutes of fame. So yes, your tax dollars did indeed likely pay for some or all of this “research.”

In one of the articles, Dr. Jeffrey R. Botkin, associate vice president for research integrity at the University of Utah, which collected the genetic information of some research participants whose identities were breached, cautioned about overreacting. “Genetic data from hundreds of thousands of people have been freely available online,” he said, “yet there has not been a single report of someone being illicitly identified.” He added that “it is hard to imagine what would motivate anyone to undertake this sort of privacy attack in the real world.” But he said he had serious concerns about publishing a formula to breach subjects’ privacy. By publishing, he said, the investigators “exacerbate the very risks they are concerned about.”

Well, it’s obvious that these folks at Whitehead institute don’t live in the real world and clearly don’t have enough real scientific research to do.

So, what is the take home of all of this?

You are not at risk of having anything exposed in this incident unless you are one of the 1000 people in the 1000 Genomes Project. If you are part of the 1000 Genomes Project, and male, there is a 12% risk that they figured out your last name and using other tools, possibly who you are, along with your family. If you are related to someone in the 1000 Genomes Project, the researchers might have figured out that you are related to them. So now the risk is that they’ll do what with that information??? Guaranteed, someone will figure out the same information and much more quickly, without your DNA and without government funding if you simply stop paying your bills.

If you participate in a research project, such as the 1000 Genomes Project, where your full results are made publicly available, you sign a release, and that release indicates that your privacy may not be able to be protected. You are aware of the risks before you begin.

We, as a community, have been warned for years not to put information that might be medically informative on the internet, such as full sequence mitochondrial DNA information. Anyone who does so, does it at their own risk. The people in the 1000 Genomes Project knowingly took that risk.

If you stay within the confines of the genealogy and DTC mainstream testing companies, you are fairly well protected. Having said that, reading the consent forms of any of the companies makes it clear that your identity is never entirely protected. We’re genealogists after all. What good is genealogical testing if you can’t contact people you match?

Inferred health risks are not the issue they are being portrayed to be in these articles. Your cousins health risks are not necessarily yours. Genetic inheritance is a complex and individual event.

Insurers who can use health information to restrict or deny insurance are simply going to request a blood sample. They are not going to act like a blood hound on the scent of a rabbit and sort through tons of information for inferences. Why would they when they can obtain the information they seek, directly and much less expensively?

For those researchers involved with information made publicly available, such at the 1000 Genomes Project, this is a wake-up call that perhaps less information available publicly is better. Some information, such as ages and location should perhaps be available only to legitimate researchers, which would still have included the Whitehead Institute people, but would have taken away much of their thunder. I understand this change has already been implemented, but that doesn’t entirely mitigate the issue of genetic data mining publicly available full genomic sequence information for identity, only makes it a little more difficult and less likely to succeed.

I clearly understand why hackers want my bank account information, and why identity thieves want my personal information, but why, in the real world, not at Whitehead institute, would anyone ever spend the time and effort to do this? The motivation for these researchers was clearly to publish, but I can think of no reason other than that or simply “because they could” to spend the time doing something like this. Who would want to and for what purpose?

The sky is not falling

It’s behind a paywall, but you can access the scientific article here that started all of this hubbub.

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Decoding and Rethinking Neanderthals

Posted on January 10, 2013 by Roberta Estes

On January 9, 2013, PBS ran a wonderful documentary, Decoding Neanderthals, about Neanderthals, what we have recently discovered about them, and what it means to us as humans. There has been a lot of discussion about this topic spurred by both the 23andMe and the Geno2.0 tests that provide a percentage of Neanderthal to participants. Geno2.0 also provides a percentage of Denisovan.

Program Description:
Over 60,000 years ago, the first modern humans—people physically identical to us today—left their African homeland and entered Europe, then a bleak and inhospitable continent in the grip of the Ice Age. But when they arrived, they were not alone: the stocky, powerfully built Neanderthals had already been living there for hundreds of thousands of years. So what happened when the first modern humans encountered the Neanderthals? Did we make love or war? That question has tantalized generations of scholars and seized the popular imagination. Then, in 2010, a team led by geneticist Svante Paabo announced stunning news. Not only had they reconstructed much of the Neanderthal genome—an extraordinary technical feat that would have seemed impossible only a decade ago—but their analysis showed that “we” modern humans had interbred with Neanderthals, leaving a small but consistent signature of Neanderthal genes behind in everyone outside Africa today. In “Decoding Neanderthals,” NOVA explores the implications of this exciting discovery. In the traditional view, Neanderthals differed from “us” in behavior and capabilities as well as anatomy. But were they really mentally inferior, as inexpressive and clumsy as the cartoon caveman they inspired? NOVA explores a range of intriguing new evidence for Neanderthal self-expression and language, all pointing to the fact that we may have seriously underestimated our mysterious, long-vanished human cousins.

I’m going to share some of the highlights of the program, but this is in no way a spoiler, as the program contains lots of visual information that just can’t be conveyed by a review.

Chris Stringer from the Natural History Museum in London introduced us to the Neanderthals. It turns out that our perception of what a Neanderthal looks like is a result in large part of skeleton that was reconstructed improperly due to advanced arthritis, causing the individual to appear to walk hunched over, much like, well, our stereotypical view of a caveman. Just goes to show what bad PR can cause.

Neanderthal skeletons can be positively identified. Their facial structure is different than that of modern man, with an identifiable brow ridge and bones that push forward in the nose and mouth region, as compared to our flatter faces today.

Neanderthals lived a short life, most were dead by age 30. They were large and strong. They participated in up-close and personal hunting, using spears, which meant they had to come in close contact with their prey.

Neanderthals began living in Europe about 300,000 years ago, having exited from Africa. They evolved to fit the European, colder, climate. It had been thought up until recently that they lacked the brainpower of humans, had no spoken language, or the ability for such, no personal ornamentation, art or evidence of ritual or religion. These are the functions that make us uniquely human and separate us from the non-human world, and we fully believed that Neanderthals lacked these defining characteristics.

We have learned differently, much as a result of genetic discoveries that tell a different story of Neanderthals.

Homo sapiens left African about 40,000 years ago, and within 10,000 years, Neanderthals, who had spread throughout most of Europe and much of Asia were gone. The map below shows the locations where fossilized Neanderthal remains have been found.

The assumption has been made that Homo Sapiens were responsible for the Neanderthals demise, either by killing them off or providing too much competition for scarce resources, outnumbering them 10 to 1.

Svante Paabo, a Swedish geneticist now at the Max Planck Institute for Evolutionary Anthropology forever changed the genetic world, how we perceive Neanderthals, and paradoxically, how we think of ourselves.

Pääbo is known as one of the founders of paleogenetics, a discipline that uses the methods of genetics to study early humans and other ancient populations.

In August 2002, Paabo published findings about the “language gene”, FOXP2, which is lacking or damaged in some individuals with language disabilities. This research would prove critical, later, in the humanization of the Neanderthal.

In 2006, he announced a plan to reconstruct the entire genome of Neanderthals. In 2007, Pääbo was named one of TIME Magazine’s 100 most influential people of the year.

In February 2009, at the Annual Meeting of the American Association for the Advancement of Science (AAAS), it was announced that the Max Planck Institute for Evolutionary Anthropology had completed the first draft version of the Neanderthal genome. Over 3 billion base pairs were sequenced in collaboration with the 454 Life Sciences Corporation. This project, led by Pääbo, shed and will continue to shed new light on the recent evolutionary history of modern humans.

In March 2010, Pääbo and his coworkers published a report about the DNA analysis of a finger bone found in the Denisova Cave in Siberia; the results suggest that the bone belonged to an extinct member of the genus Homo that had not yet been recognized, the Denisova hominin.

In May 2010, Pääbo and his colleagues published a draft sequence of the Neanderthal genome in the journal Science. Below, a scientist at Max Plank extracting Neanderthal DNA.

Paabo shared in the program that many times during the Neanderthal sequencing project, he himself “despaired many times of being able to do it”, doubting that it could be done. It took a total of 4 years. The team found good candidates, 3 well-preserved female bone fragments from the Vindija Cave in Croatia.

Because of the age of the fragments, and because they had been in the ground for so long, much of the DNA recovered wasn’t Neanderthal, but that of bacterial organisms and fungus. The team developed a method to eliminate the bacteria, leaving only Neanderthal DNA. However, those genetic fragments still had to be reassembled, piece by piece, like a huge jigsaw puzzle with no picture on the box, into the Neanderthal genome.

Four long years later, the puzzle was finished. I hope the team had a very big celebratory party!

Ed Green, a scientist on Paabo’s team said that the first thing the scientists looked for was to determine whether or not Neanderthals had the FOXP2 gene for language, and if so, is it identical to the human version, or is it different. The answer was that it was identical to the language gene carried by Homo Sapiens, modern humans. This tells us not only that Neanderthals had the capabilities for language, but that this gene evolved in Africa, before Neanderthals left, 300,000 years ago.

The next question, of course, was whether or not modern humans carried any DNA that could be labeled as Neanderthal. In other words, the question of inter-species breeding arose. It was believed that this was impossible, because two different species cannot have fertile offspring. This was proven to be an inaccurate assumption relative to Neanderthal and Homo Sapiens.

Paabo’s team sequenced the DNA of 5 individuals from different parts of the world. They isolated parts of the Neanderthal DNA that were measurably different from that of modern humans. In other words, those sequences could be positively identified as Neanderthal. Compared against the DNA of the 5 contemporary individuals, only the person from Africa had none of the Neanderthal DNA.

Paabo didn’t believe the results, thought they might be an artifact of statistical error or the result of not enough data, so he had his team repeat the exercise with different people, again, and again, and again, and every time, the results came back the same. Neanderthals and humans inbred, and to the degree that there is Neanderthal DNA in every population on every continent outside of Africa today.

John Hawks, an anthropologist at the University of Wisconsin used jelly beans to illustrate Neanderthal DNA in worldwide populations today. It turns out that the Chinese have the least amount, with about 1% and the people of Tuscany have the most, with about 4%. So the mountainous areas of Europe and Italy were a hotbed of Neanderthal activity and human interbreeding.

This caused other experts to think again about the Neanderthals in what could be called a radical shift in perspective. All of a sudden, when we realized that they were part of us, they became more human to us. They could and probably did have speech, so they could and probably did other “human” things too.

Joao Zilhao, a paleolithic archaeologist at the University of Bristol, also a flintknapper, spent years reconstructing the process of making Neanderthal tools, what were once believed to be scraps of flint with sharp edges. He proved, among other things, that obtaining these “scraps” involved a complex process of very specific flintknapping strokes. This skill was far from the previously perceived unintelligent caveman, and furthermore, it likely required language instruction.

Another early technology, in use 250,000 years ago, involved a complex process to create a type of pitch to secure spearheads to spear shafts.

The Neanderthals began evolving before our very eyes.

Michael Walker, a professor of Zoology and Physical Anthropology at the University of Murcia, discovered indeed that Neanderthals likely did have ceremony and ritual, the hallmarks of religion, which involved the ability for complex thought and reasoning. Shells and bones, drilled or punched to be worn as ornaments have been identified, along with pigments believed to have been used as body paints.

We still do this today; look at the fans at any football game.

In addition, it appears that a burial may have been found in Spain, along with two panther paws. Michael mentioned them as a trophy, I thought more in terms of spiritual significance.

John Hawks discussed what the Neanderthal parts of our genome have done for humans. Many of the Neanderthal genes have no known purpose, but there is one significant exception. It’s somehow ironic that we may indeed have survived as a species in a foreign environment, colder Europe, thanks to inbreeding with the Neanderthals. Humans carry a very specific Neanderthal piece of DNA that is essential to the immune system’s ability to attack viruses and bacteria, the HLA or Human Leukocyte Antigen. Because individuals who carried HLA might well have survived when others didn’t, the HLA became naturally selected for, and therefore present in the descendant population, us, “saving lives to this day.’

As John said, we are just beginning to understand our debt to the Neanderthals. Not only that, we also are rethinking what extinction really meant. We have presumed that Neanderthals went extinct, or died out, because we could no longer find their remains in fossil evidence. Perhaps, as Mark Twain said “reports of my demise have been greatly exaggerated.”

Is the reason we could no longer find separate Neanderthals because they interbred and assimilated into the Homo Sapiens population who were probably the dominant species, outnumbering them ten to one? Was their extinction not a dying out at all, but an absorption? Perhaps that was simply the natural progression of things, or maybe they realized that their recipe for success, for long-term survival, was not to remain separate, but to become part of the larger population. In fact they do survive today in just that way, as a part of all of us outside of Africa.

Decoding Neanderthals is available to watch online at http://www.pbs.org/wgbh/nova/evolution/decoding-neanderthals.html

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Autosomal Testing Comparison

Posted on January 3, 2013 by Roberta Estes

Currently, there are four different entities, 3 corporations and a nonprofit, that test autosomal DNA using the newest technology, the Illumina chip. There are different features and functions of each one.

I am describing them below in broad terms, and including links to articles where I and others have discussed their autosomal products.

23andMe – The first company to enter the chip based world of genetic processing by introducing a health traits and genealogy product that provided genealogists with cousin matches and percentages of ethnicity. They provide raw data files that can be downloaded and then uploaded to Family Tree DNA and GedMatch. In December 2012, after a significant capital investment, they dropped the price of their autosomal product to $99 with a goal to reach one million customers as a result. They currently have about 180,000.

http://dna-explained.com/2012/12/07/new-worldview-at-23andme/

Family Tree DNA – Clearly the leader in genetic genealogy testing, they offer the Family Finder test using the same chip based platform as 23andMe. Customers of 23andMe can upload their raw data file to Family Tree DNA for $89, effectively allowing them to fish in both pools for cousin matches and to obtain the ethnicity predictions from both companies. Family Tree DNA provides raw data files and numerous tools to assist the genealogist, including integrated searching of autosomal, Yline and mitochondrial matches. The Family Tree DNA Family Finder product is currently $199. Family Tree DNA customers are generally interested in genealogy, while 23andMe clients are often only interested in the health traits aspect of their test.

http://dna-explained.com/2012/10/14/what-to-order-geno-2-0-vs-family-tree-dna-products/

Ancestry – Ancestry introduced their AncestryDNA test in early 2012 by initially giving away tests, then selling tests for the reduced price of $99 to build their autosomal data base. Today, the tests range from $129 to $199 depending on whether or not you have an Ancestry.com subscription. Continued, complete access hinges upon maintaining a subscription at some level. Their test reports cousin matches and percentages of ethnicity. If your matches have attached their genealogy, and it’s not marked private, you can see if you share common ancestors by viewing their tree. Ancestry’s ethnicity predictions have significant issues, they provide no autosomal tools, such as a chromosome browser for cousin matching and they do not provide your raw data to download, although they have said they will provide that sometime in 2013.

http://dna-explained.com/2012/10/24/ancestrys-mythical-admixture-percentages/

http://dna-explained.com/2012/09/10/ancestry-autosomal-results-are-back/

http://www.isogg.org/wiki/AncestryDNA

National Geographic Genographic 2.0 – The latest autosomal test to be released is focused somewhat differently that the other tests. This test looks more at deep ancestry using the discoveries made within the Genographic project over the past 6 years. This test provides the deepest clade testing for the Y chromosome available from any test at any company. It also provides ethnicity percentages based on many newly discovered SNPs not in use elsewhere. The price is $199.

http://dna-explained.com/2012/07/25/national-geographic-geno-2-0-announcement-the-human-story/

http://dna-explained.com/2012/07/26/geno-2-0-qa-with-bennett-greenspan/

http://dna-explained.com/2012/07/30/geno-2-0-answers-from-spencer-wells/

http://dna-explained.com/2012/12/11/geno-2-0-results-first-peek/

http://dna-explained.com/2012/12/12/geno-2-0-results-kicking-the-tires/

In addition, Debbie Kennett has added a wiki page about comparing autosomal testing companies in the ISOGG Wiki at:

http://www.isogg.org/wiki/Autosomal_DNA_testing_comparison_chart

Thanks Debbie for your efforts to help everyone!

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2012 Top 10 Genetic Genealogy Happenings

Posted on December 28, 2012 by Roberta Estes

2012 has been a very busy year for genetic genealogists. There have been lots of discoveries and announcements that affect everyone, now and in the future. The watchwords for 2012 would be “churn” and “explosive growth.” Let’s take a look at the 10 most important events, why they are important and what they mean for the future of genetic genealogy.

These items are in what I think are relatively good order, ranked by their importance, although I had a very difficult time deciding between number 1 and 2.

1. The New Root – Haplogroup A00

At the Family Tree DNA conference in November, Michael Hammer, Bonnie Schrack and Thomas Krahn announced that they had made a monumental discovery in the age of modern man known as Y-line Adam. The discovery of Haplogroup A00 pushes the “birth” of mankind back from about 140,000 years ago to an amazing 338,000 years ago. Utterly amazing. The DNA came from an American family from South Carolina. This discovery highlights the importance of citizen science. Bonnie is a haplogroup administrator who recognized the potential importance of one of her participants’ DNA. Thomas Krahn of course is with Family Tree DNA and ran the WTY test, and Michael Hammer is at the University of Arizona. So you have the perfect blend here of participant, citizen scientist, commercial lab and academia. What was never thought possible a decade or so ago is not only working, it’s working well and changing the face of both science and humanity.

http://dna-explained.com/2012/11/16/the-new-root-haplogroup-a00/

http://www.haplogroup-a.com./

2. Geno 2.0

Geno 2.0 is the Nickname for the National Geographic Society’s Genographic Project version 2.0. That mouthful is why it has a nickname.

This amazing project has leveraged the results of the past 7 years of research from the original Genographic project into a new groundbreaking product. Geno 2.0, utilizing the GenoChip, a sequencing chip created specifically for Nat Geo, offers the most complete Y tree in the world today, expanding the SNP tree from just over 800 SNPs to over 12,000. They are in essence redrawing the Y chromosome tree as I write this. In addition, the person who purchases Geno 2.0 will receive a mitochondrial DNA haplogroup assignment. Over 3300 new mitochondrial mutations were discovered. A brand new anthropological “percentages of ethnicity” report is featured based on over 75,000 Ancestry Informative Markers, many only recently discovered by the Genographic project. Additionally, participants will receive their percentage of both Neanderthal and Denisovan ancestry based on 30,000 SNPs identified that signal interbreeding between the hominids. A new website will also facilitate social networking and uploading information to Family Tree DNA.

The wonderful news is that there is a massive amount of new information here that will change the landscape of genetic genealogy. The difficulty is that we are struggling a bit under the load of that massive amount of information that is just beginning to descend upon us. It’s a great problem to have!

http://dna-explained.com/2012/07/25/national-geographic-geno-2-0-announcement-the-human-story/

http://dna-explained.com/2012/07/26/geno-2-0-qa-with-bennett-greenspan/

http://dna-explained.com/2012/07/30/geno-2-0-answers-from-spencer-wells/

http://dna-explained.com/2012/07/31/geno-2-0-wty-mtdna-full-sequence-participants-and-more/

http://dna-explained.com/2012/10/14/what-to-order-geno-2-0-vs-family-tree-dna-products/

http://dna-explained.com/2012/10/16/geno-2-0-the-kit-arrives/

http://dna-explained.com/2012/12/11/geno-2-0-results-first-peek/

http://dna-explained.com/2012/12/12/geno-2-0-results-kicking-the-tires/

3. Reconstructed Sapiens Reference Sequence (RSRS)

In July, Family Tree DNA implemented the RSRS that in effect reconstructs the genetic profile of Mitochondrial Eve and bases the comparison of our DNA today against the RSRS sequence as opposed to the Cambridge Reference Sequence (rCRS) created in 1981 that is or was the current standard. The RSRS is a result of the watershed paper published in April 2012 by Dr. Doron Behar and 8 other authors titled “A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root.” A complementary research website, www.mtdnacommunity.org, accompanies the paper.

http://dna-explained.com/2012/07/14/what-happened-to-my-mitochondrial-dna/

http://dna-explained.com/2012/07/15/the-crs-and-the-rsrs/

http://dna-explained.com/2012/07/16/the-mtdna-community/

http://dna-explained.com/2012/12/02/little-a-big-a-mitochondrial-dna/

4. Full Genome and Exome Sequence Offered Commercially by Gene by Gene

It was announced at the November DNA conference that Gene by Gene, the parent company of Family Tree DNA, through their division titled DNA DTC is offering full genomic sequencing for the amazing price of $5495 for the full genome and $695 for the exome. This is a first in the consumer marketspace. Today, this doesn’t have a lot of application for genetic genealogy, but as the price continues to drop, and utilities are built to process the full genomic data, certainly a market and applications will emerge. This is an important step forward in the industry with a product that still cost 3 million dollars in 2007.

http://dna-explained.com/2012/11/30/gene-by-gene-announces-landmark-dna-dtc-full-genome-sequence/

5. Neanderthal and Denisovan DNA

It’s official – they did it. Yep, they interbred and well, they are not them anymore, they are us. Given that everyone in Asia and Europe carries a part of them, but not people from Africa, it would appear that two populations admixed rather thoroughly in Eurasia and/or the populations were small. The amount of Neanderthal and Denisovan DNA will continue at approximately the proportions seen today in Europe (2% Neanderthal) and Asia unless a significant amount of admixture from a population (Africa) that does not carry this admixture is introduced. So if you’re European, you carry both Neanderthal and Denisovan DNA. They are your ancestors. The good news is that you can find how much of each through the Geno 2.0 test. 23andMe results give you the percentage of Neanderthal, but not Denisovan.

http://dna-explained.com/2012/08/31/denisovan-dna-tells-a-story/

http://dna-explained.com/2012/12/12/geno-2-0-results-kicking-the-tires/

6. Ancestral Genome Reconstruction Begins, Led by Falling Autosomal Prices and the Ability to Fish in Multiple Ponds

2012 has been the year of autosomal testing price reductions and a great deal of churn in this marketspace. Companies are playing leap-frog with one another. However, sometimes things are not all that they seem.

Initially, 23andMe opted for an initial payment plus monthly subscription model, which they abandoned for a one time payment price of $299 in early 2012. Family Tree DNA was slightly less, at $289.

Ancestry led the price war by giving away kits, then selling them for $99, then $129 plus a subscription as an entrance into this market. However, looking at the Ancestry consent form hints at possible reasons why they were selling below the cost of the tests. You are in essence giving them permission to sell your DNA and associated information. In addition, to gain full access to your results and matches, you must maintain some level of subscription to Ancestry.com, increasing the total effective price.

Next came Family Tree DNA’s sale where they dropped their autosomal price to $199, but they were shortly upstaged by 23andMe whose price has now dropped to $99 permanently, apparently, a result of a 50 million dollar investment in order to reach 1 million customers. They currently have about 180,000. 23andMe has always been in the medical/health business, so their clients have always understood what they were consenting to and for.

Not to be outdone, Family Tree DNA introduced the ability earlier in 2012 to upload your data files from 23andMe to FamilyTree DNA for $89, far less than a second test, which allows you to fish in a second pond where genealogists live for matches. The challenge at 23andMe is that most of their clients test for the health traits and either don’t answer inquiries or match requests, or know little about their genealogy if they do. At Family Tree DNA, matches don’t have to answer and allow a match, testers are automatically matched with all participants who take the Family Finder test (or upload their 23andMe results) and testers are provided with their matches’ e-mail address.

Of course, Geno 2.0 was also introduced in the midst of this, in July, for $199 with the additional lollipop of new SNPS, lots of them, that others simply don’t have access to yet.

The good news is that consumers have benefitted from this leapfrogging, I think. Let’s hope that the subsidized tests at Ancestry and 23andMe don’t serve long term to water down the demand to the point where unsubsidized companies (who don’t selling participants genetic results to others) have problems remaining viable.

Personally, I’ve tested at all of these companies. I’ll be evaluating the results shortly in detail on my blog at www.dna-explained.com.

The tools provided by most testing companies, plus GedMatch, and multiple ponds to fish in are allowing the serious genetic genealogist to “reconstruct” their genome, attributing segments to specific ancestors. Conversely, we will also be able to “reconstruct” specific ancestral family lines as well by identifying autosomal segments in multiple descendants. This new vision of autosomal genetic genealogy will allow much more accurate ancestral line matching, and ancestor identification in the not-so-distant future.

http://www.yourgeneticgenealogist.com/2012/01/family-tree-dna-now-accepting-23andme.html

http://www.yourgeneticgenealogist.com/2012/05/23andme-eliminates-subscription-model.html

http://www.yourgeneticgenealogist.com/2012/10/clarification-of-what-is-available-to.html

http://www.yourgeneticgenealogist.com/2012/12/23andme-receives-50-million-and-drops.html

http://www.thegeneticgenealogist.com/2012/12/26/23andme-and-labcorp-sued-for-patent-infringement/

7. Ethnicity Tests Mature – Minus 1

The good news is that the various ethnicity tests (known as BGA or biogeographical ancestry tests) that provide participants with their percentages of various world populations are improving. The bad news is that there is currently one bad apple in the card with very misleading percentages – and that is Ancestry.com.

23andMe introduced a new version of their ethnicity product in December, expanding from only 3 geographic categories to several. The Geno 2.0 test results are just beginning to be returned which include ethnicity predictions and references to several base populations.

Family Tree DNA finally has some competition in this arena where for years they have been the only serious player, although opinions differ widely about which of these three organizations results are the most accurate. All four are Illumina chip based, using hundreds of thousands of locations, as compared with the previous CODIS type tests which used between 15 and 300 markers and are now outdated. All companies use different reference populations which, of course, provide somewhat different results to participants. All companies, except Ancestry, have documented and shared their reference population information.

Outside of these companies, Doug McDonald offers a private analysis and Gedmatch offers a series of BGA comparisons written by third parties.

While this industry continues to grow and mature, I’m thinking about just averaging the autosomal ethnic results and calling it good:)

http://dna-explained.com/2012/07/21/ethnicity-finders/

http://dna-explained.com/2012/10/24/ancestrys-mythical-admixture-percentages/

http://dna-explained.com/2012/12/07/new-worldview-at-23andme/

http://dna-explained.com/2012/09/09/doug-mcdonald-on-biogeograpical-analysis/

http://dna-explained.com/2012/12/11/geno-2-0-results-first-peek/

http://www.yourgeneticgenealogist.com/2012_12_01_archive.html

8. Finding Your Roots PBS Series with Henry Louis Gates

PBS sponsored a wonderful series in the spring of 2012 hosted by Henry Louis “Skip” Gates, the chair of African American Studies at Harvard. This series followed a lesser known 2010 series. The 2012 inspirational series reached tens of thousands of people and increased awareness of genetic genealogy as well as sparked an interest in genealogy itself, especially for mixed race and African American people. I was disappointed that the series did not pursue the Native American results unexpectedly obtained for one participant. It seemed like a missed opportunity. Series like this bring DNA testing for genealogy into the mainstream, making it less “strange” and frightening and more desirable for the average person. These stories were both inspirational and heartwarming. I hope we can look forward to similar programs in the future.

http://en.wikipedia.org/wiki/Finding_Your_Roots

CeCe Moore covered this series in March and April on her blog.

http://www.yourgeneticgenealogist.com/2012/03/finding-your-roots-with-henry-louis.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_09.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_16.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_23.html

http://www.yourgeneticgenealogist.com/2012/04/finding-your-roots-with-henry-louis_30.html

9. Ancestry, GeneTree and Sorenson

GeneTree, a for profit company and Sorenson, a non-profit company were both purchased by Ancestry.com. This was about the same time as Ancestry introduced their autosomal AncestryDNA product. Speculation was that the autosomal results at Sorenson might be the foundation for the new autosomal test comparisons, although there has been no subsequent evidence of this.

Ancestry initially gave away several thousand kits in order to build their data base, then sold thousands more for $99 before raising the price to what appears to be a normalized price of $129 plus an annual ancestry subscription.

While GeneTree was never a major player in the DNA testing marketspace, Sorenson Molecular Genealogical Foundation played an important role for many years as a nonprofit research institute. There was significant distress in the genetic genealogy community related to the DNA contributed to Sorenson for research being absorbed by Ancestry as a “for profit” company. Ancestry is maintaining the www.smgf.org website, but no additional results will be added. Sorenson has been entirely shuttered. Many of the Sorenson/GeneTree employees appear to have moved over to Ancestry.

The initial AncestryDNA autosomal product offering is poor, lacks tools and the ethnicity portion has significant issues. It’s strength is that many people who test are already Ancestry subscribers and have attached their trees. So you can’t see how you connect genetically to your matches (lack of tools), but you can see the trees, if they are attached and not marked as private, of those with whom you match. Ancestry provides “hints” relative to matching individuals or surnames.

Eventually, if Ancestry improves its products, provides tools and releases the raw data to consumers, this may be a good thing. It’s an important event in 2012 because of the massive size of Ancestry, but the product is mediocre at best. Ancestry seems unwilling to acknowledge issues unless their feet are held to the fire publicly as illustrated with a “lab error” erroneous match for an adoptee caught by the consuming public and ignored by Ancestry until CeCe Moore exposed them in her blog. Whether Ancestry ultimately helps or hurts the genetic genealogy industry is a story yet to be told. There is very little positive press in the genetic genealogy community surrounding the Ancestry product, but with their captive audience, they are clearly going to be a player.

http://www.yourgeneticgenealogist.com/2012/05/ancestrycom-buys-genetree-and-launches.html

http://dna-explained.com/2012/07/12/did-you-test-at-genetree/

http://dna-explained.com/2012/08/30/is-history-repeating-itself-at-ancestry/

http://dna-explained.com/2012/07/18/the-trouble-with-ancestry-com-matches/

http://dna-explained.com/2012/08/14/y-dna-family-tree-dna-vs-ancestry/

http://dna-explained.com/2012/08/16/ancestrys-consent-form-for-ancestrydna-autosomal-test/

http://dna-explained.com/2012/09/10/ancestry-autosomal-results-are-back/

http://dna-explained.com/2012/10/15/ancestrys-dna-survey/

http://dna-explained.com/2012/10/23/ancestry-to-release-array-data-in-2013/

http://dna-explained.com/2012/10/24/ancestrys-mythical-admixture-percentages/

http://www.thegeneticgenealogist.com/2012/06/19/problems-with-ancestrydnas-genetic-ethnicity-prediction/

http://www.yourgeneticgenealogist.com/2012/08/ancestrydna-confusing-relationship.html

http://www.yourgeneticgenealogist.com/2012/08/follow-up-on-ancestrydna-and-adoptees.html

http://www.yourgeneticgenealogist.com/2012/09/23andme-says-no-match-for-adoptees.html

10. GedMatch

GedMatch, www.gedmatch.com, created by John Olson and Curtis Rogers, isn’t new in 2012, but it’s maturing into a tool that is becoming the defacto workhorse of the serious autosomal community. People who test at either 23andMe or Family Tree DNA download their raw results and other match information and then use a variety of tools at GedMatch to look at results in different ways and using different thresholds. GedMatch is currently working to accept the newly arriving Geno 2.0 data files. Ancestry does not at this time allow their customers access to their raw data files, so there is nothing to upload. The bad news is that not everyone downloads/uploads their information. Only the most savvy users, and the download/upload is not always a smooth process, often necessitating several attempts, a magic wand and some fairy dust for luck.

GedMatch is a volunteer effort funded by donations on the GedMatch site. The magnitude of this project came to light when they needed new servers this year because the amount of traffic disabled their internet service provider. It may be a volunteer effort, but it has mainstream requirements. Therefore, while occasionally frustrating, it’s easy to understand why it’s light on documentation and one has to poke around a bit to figure things out. I would actually prefer that they make it a subscription site, clean up the bugs, add the documentation and take it to the next level. It would also be very nice if they could arrange something with the major players in terms of a seamless data transfer for clients. All told, it’s an amazing contribution as a volunteer site. Hats off to Curtis and John for their ongoing contribution to genetic genealogists!!!

www.gedmatch.com

http://www.legalgenealogist.com/blog/2012/08/12/gedmatch-a-dna-geeks-dream-site/

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Proving Native American Ancestry Using DNA

Posted on December 18, 2012 by Roberta Estes

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Every day, I receive e-mails very similar to this one.

“My family has always said that we were part Native American. I want to prove this so that I can receive help with money for college.”

The reasons vary, and not everyone wants to prove their heritage in order to qualify for some type of assistance. Some want to find their tribe and join to reclaim their lost heritage. Some want to honor their persecuted and hidden ancestors, undoing some of the wickedness of the past, and some simply seek the truth. Regardless of why, they are all searching for information lost to them.

I’d like to talk about three topics in proving Native Ancestry. First, I’d like to do some myth-busting. Second, I’d like to talk a little about conventional research and third, I’d like to discuss what DNA can, and can’t, do for you.

As you read this blog, please click on the links. I’m not going to repeat something I’ve already covered elsewhere.

Myth-Busting

Myth 1 – Free College

There is no free college for Native Americans. There are sometimes scholarships and grants available, mostly by the individual tribes themselves, for their official members.

Myth 2 – Joining a Tribe

Many people think that if they can only figure out which tribe their ancestor descends from, they can join. This is untrue. Each tribe is a sovereign nation, and they get to determine their criteria for membership. Most tribes require a specific percentage of Native “blood,” called blood quantum, in addition to being able to document which tribal member you descend from. Some tribes require as much as 25% Native heritage, and most require at least 1/16^th Native heritage, which is one great-great grandparent. If you don’t know who in your family was a tribal member it’s unlikely that you would be able to meet the blood quantum requirement.

Myth 3 – DNA Testing Will Reveal my Tribe

Generally, DNA testing does not provide us with the information needed to determine a tribe, although it can clearly tell, using y-line or mitochondrial DNA testing, whether your direct paternal or maternal line was or was not Native. Sometimes you will be able to infer a tribe based on your matches and their documented history, but the definition of tribes, their names and locations have changed over time. We are working on improving this ability, but the science simply isn’t there yet and the number of Native people who have tested remains small.

Simply put, most federally recognized tribes aren’t interested in more tribal members. More members mean a smaller piece of the pie for existing members. The pot of resources, whatever resources you’re discussing, is only so large and it must be shared by all tribal members.

What is a Tribe?

Tribes in the US fall into two categories. When most people think about tribes they are talking about federally recognized tribes. Those are tribes that have some continuity with the past, such as they have always been a tribe, or they still retain tribal lands, etc., and the federal government recognizes them as such. These are the tribes that qualify for government programs and many own casinos. As you might imagine, with the influx of casino money, the desire to join a tribe has increased significantly.

The second category is non-federally recognized tribes. Some are state recognized and others, not at all. State recognition does not in any way guarantee federal or state funding and there are no universal standards for state recognition. In other words, your mileage may vary, widely. Non-federally recognized tribes are often run as non-profit entities. In many cases, these tribes will help people research and document their genealogy and may be more open to tribal membership for those connecting with their Native heritage.

Be aware that some “tribes” that fall into the non-federally recognized category may be less than ethical. Some tend to come and go. In one case, to apply to join, one had to provide information such as social security numbers and a complete family pedigree including your children. In some cases, membership is very expensive, hundreds of dollars, but is available to almost anyone for the right price. When evaluating tribes that are not federally recognized, if something sounds fishy, it probably is. Caution is the watchword.

In general, the federally recognized tribes do not feel kindly towards the non-federally recognized tribes and view them as “fake,” interlopers trying to get part of that pie. Of course, the non-federally recognized tribes feel differently; that they are reclaiming their heritage denied them. Native American politics is nothing new and is fraught with landmines.

No federally recognized tribes, to the best of my knowledge, have considered DNA testing as a criteria for membership. No federally recognized tribe has endorsed or participated in DNA testing that I’m aware of. This does not mean that individuals have not privately tested.

Traditional Genealogy Research

Given the criteria for membership in federally recognized tribes, traditional genealogy is the only way to obtain the type of information required. If your family history includes a tribal name, and east of the Mississippi, that most often is Cherokee, contact the various Cherokee tribes to inquire about membership criteria. If the membership criteria is 25% blood quantum, and you must live on the reservation, you’re toast…..no need to continue that line of research if your goal is to join the tribe.

If your goal is simply to find your Native ancestor, that’s another matter entirely. Begin by using the traditional research tools.

First, look at where your ancestor or that family line was located. Did they migrate from elsewhere? How were they listed in the census? Was someone listed as other than white, indicating mixed race? Check the records where they lived, tax records and others to see if there is any indication of non-European heritage. Remember that your non-white ancestor would have retained their “darker” countenance for at least 2 generations after being admixed. Many Native people were admixed very early.

So first, check the normal genealogy records and look for hints and traces of non-European ancestry.

Second, turn to Native resources that might reflect the Native people in the areas where your family is or was found. The Access Genealogy site is absolutely wonderful and has an amazingly complete set of records including searchable tribal rolls. In addition, I add information almost daily to the Native Heritage Project at www.nativeheritageproject.com, which is searchable. There are many more resources including several collections at Ancestry.com.

Hopefully, these records will help narrow your focus in your family tree to a particular person or two, not just a general branch. Family rumors like “Grandma was a Cherokee Princess” are particularly unuseful. What they more likely mean is that there was indeed some Native ancestry someplace in her line. Cherokee has become a generic word like Kleenex. It may also have meant that Indian heritage was claimed to cover much less desirable African heritage. Institutionalized discrimination existed against any people of color in pre-1967 America, but Indians generally retained some rights that people of African ancestry did not. Laws varied by state and time. Take a look at my blog about Anti-Miscegenation Laws and when they were overturned.

Now, let’s look at DNA testing to see what it can do for you.

DNA Testing to Prove Native Ancestry

There are three types of DNA testing that you can do to prove Native Ancestry. Two are very focused on specific family lines, and one is much more general.

Mitochondrial for your direct maternal line.
Y-line for your direct paternal line – if you are a male. Sorry ladies.
Autosomal to test your ethnic mix and one direct marker test for Native ancestors.

On a pedigree chart, these genealogical lines look like this:

You can see the path that the blue Y chromosome takes down the paternal line to the brother and the path the red mitochondrial DNA takes down the maternal line to both the brother and the sister. Autosomal tests the DNA of all of the 16 ancestral lines shown here, but in a different sort of way.

Let’s look at each type of testing separately.

Y-Line DNA – For Paternal Line Testing for Males

The Y-line testing tests the Y chromosome which is passed intact from father to son with no DNA from the mother. This is the blue square on the pedigree chart. In this way, it remains the same in each generation, allowing us to compare it to others with a similar surname to see if we are from the same “Smith” family, for example, or to others with different surnames, in the case of adoption or Native heritage. Native American genetics isn’t terribly different than adoptees in this situation, because different English surnames were adopted by various family members, into the late 1800s and sometimes into the early 1900s, depending on the location.

Y-line DNA can tell you whether or not you descend from a common male genealogically when compared to another testing participant. Small mutations do take place and accumulate over time, and we depend on those so that we don’t all “look alike” genetically. It can also tell you by identifying your deep ancestral clan, called a haplogroup, whether or not you descend from early Native Americans who were here before contact with Europeans. For that matter, it can also tell you if you descend from those of African, European or Asian ancestry.

Scientists know today that there are only two primary haplogroups indicating deep ancestry that are found among Native American males who were here prior to contact with Indo-Europeans, and those haplogroups are C and Q3. It is not accurate to say that all C and Q3 individuals exist only in the American Native population, but the American Native population is part of the larger group worldwide that comprises C and Q3. We find some haplogroup C and Q3 in Europe but none in African populations, although we do learn more every single day in this infant science.

This sometimes becomes confusing, because the single most common male haplogroup among current Cherokee tribal members who have tested is R1b. How can this be, you ask? Clearly, one of three possibilities exists:

The Cherokee (or those tribes who were assimilated into the Cherokee) adopted a European male into the tribe or a European male fathered a child that was subsequently raised as Cherokee.
The R1b ancestor was not adopted into the tribe, maintained their European/American identity but married a Cherokee individual woman and their descendants are recognized as Cherokee today.
There is some level of R1b admixture in the Native population that preceded contact with Europeans that we have not yet identified.

Because of the unique haplogroups for Native Americans who preceded European contact, Y-line is the only way to positively confirm that a specific line is or is not of Native American descent. This obviously applies to all of the individuals in the pedigree chart who directly descend from the oldest known ancestor in this paternal line.

Y-line testing does not indicate anything about the contributions of the other ancestors in this family tree. In other words, you could be 3/4^th Native, with only the direct paternal line being European, and this test would tell you nothing at all about those other three Native lines.

When ordering DNA tests at Family Tree DNA, which is where I recommend that you test, everyone is encouraged to join projects. There are several types of projects, but to begin with, you should join your surname project. Not only does this group you with others whom you are likely to match, but this also assures that you receive the project based discounts. I blogged about how to find and join relevant projects.

You can test at 12, 25, 37, 67 or 111 marker “locations” on the Y chromosome. I generally recommend 37 or 67 to begin which gives you enough to work with but isn’t terribly expensive. At Family Tree DNA, you can always upgrade later, but it’s less expensive in total to test more initially.

Family Tree DNA provides significant tools for Y-line DNA as well as Mitochondrial DNA. At Family Tree DNA, for all their tests, you are provided with the e-mail addresses of your matches. At Ancestry and 23andMe, you contact matches through their internal message system. My experience has been that direct e-mails have a better response rate.

The person looking for Native Heritage will be most interested in their haplogroup designation. If your haplogroup is either Q or C, you’ll want to join your haplogroup project, minimally, as well as other relevant Native American projects, and work with the administrators for further testing. Remember, neither haplogroup Q nor C are always Native, so deeper testing may be in order. You may also match others with confirmed Native heritage, including a tribe.

If the haplogroup is not Native, then you’ll have to take a look at possible reasons why.

One can never interpret non-Native haplogroup results of any one line to answer the much broader questions of, “do I have Native heritage”, “how much” and “where?” What you can do at that point is to continue to test other lines in order to discover the identity of your Native American ancestor.

Obviously, the Y-line test is only for males. Ladies, I feel your pain. However, these next tests are for both sexes.

Mitochondrial DNA – For Direct Maternal Line Testing for Both Sexes

Mitochondrial DNA is inherited by all children from their mother only, with no admixture from the father. Women obtain their mitochondrial DNA from their mother, who got it from their mother, on up the line into infinity. This is the red circle on the right hand side of the pedigree chart. Like Y-line DNA, mitochondrial DNA is passed intact from one generation to the next, except for an occasional mutation that allows us to identify family members and family lines.

Unfortunately, it does not follow any surname. In fact the surname changes with every generation when women marry. This makes it more challenging to work with genealogically, but certainly not impossible. Because of the surname changes in every generation, there are no “surname” projects for mitochondrial DNA, per se, but there are other types of projects. For example, the Mothers of Acadia project is using mitochondrial DNA to reconstruct the Acadian families including those of Native American heritage.

There are three levels of testing you can take for mitochondrial DNA at Family Tree DNA, which is where I recommend that you test. The mtDNA, the mtDNAPlus and the Full Sequence. The mtDNA test is a starter test that will provide you with a base haplogroup, but will leave people searching for Native ancestry needing a more complete test for full haplogroup identification confirming Native ancestry. I strongly recommend the full sequence test, but if the budget just won’t allow that, then the mtDNAPlus will do until you can afford to upgrade. Family Tree DNA is the only major lab that tests the full sequence region, plus, they have the largest matching data base in the industry.

To put this in perspective for you, the mtDNA and the mtDNAPlus tests both test about 10% of your mitochondrial DNA and the full sequence test tests all of your 16,569 mitochondrial locations. You can then compare them with other people who have taken any of those 3 tests. Pricing for the mtDNAPlus is currently $139 and the full sequence is $199.

MtDNA testing is not as popular as Y-line testing because it’s more difficult to use genealogically as last names change every generation. When you look at your matches, you have no idea whatsoever if you might be related to these people in a genealogically relevant time frame by looking at their last names. Those who have invested the effort to collaboratively work on their mtDNA matches, assuming a full sequence match and a shared geographical history as well, have been pleasantly surprised by what they’ve found.

A haplogroup assigning deep ancestry is provided through mitochondrial testing, so like the Y-line, depending on the haplogroup assigned, you will know if your ancestors were here before European contact. Maternal haplogroups that indicate Native heritage include A, B, C, D and X. Like Y-line DNA testing, none of these haplogroups are exclusive to Native Americans, so a full sequence level test will be required to confirm a Native American subgroup.

After you receive your results, you can enter the mtDNA and mtDNAPlus portions into public data bases. There are no public data bases for the full sequence segment because there may be medical implications in some of those mutations, so they are not displayed publicly although they are compared privately within the Family Tree DNA data base. You will want to enter your data and check for matches at www.mitosearch.org (upload directly from your matches page at Family Tree DNA), www.smgf.org and www.ancestry.com, although beware of Ancestry’s accuracy issues.

Update: As of 2019, mitosearch and SMGF no longer exist and Ancestry no longer sells Y and mitochondrial DNA tests, having destroyed their database.

Testing the Y-line and mitochondrial DNA individually gives us a great deal of very specific information about 2 lines in your pedigree chart. The best method of identifying Native American ancestors is indeed to test as many lines on your DNA pedigree chart using this methodology as possible. Let’s take a minute to look at how to create a DNA pedigree chart.

DNA Pedigree Chart

If your Y-line and mitochondrial DNA have proven not to be Native, that doesn’t mean that the rest of your lines aren’t.

Let’s take a look at how to create a DNA pedigree chart so that you can focus your Y-line and mitochondrial DNA testing for other lines.

The purpose of a DNA pedigree chart is to provide guidance in terms of inheritance and also to provide a way of documenting your progress. My chart is shown below, as an example.

You can see the Y-line of my father and the mitochondrial line of my mother, on both ends of the pedigree chart. At the top of each line, I have recorded the haplogroup information for each family. Color coding each line helps in tracking descendants who would carry the DNA of the ancestor of that line. For example, my mother’s father’s mother’s line is the yellow Miller line. I need to find a daughter of my grandfather’s sisters, or their children, or their daughter’s children, to test for that mitochondrial DNA line. Which reminds me, I need to call my cousin. Family reunions, picnics and holidays are great for this type of thing. Sadly, so are funerals.

I blogged about how to put together your own DNA pedigree chart. If you’re Native and adopted, then refer to the adoptee blog instead, or in addition.

But sometimes, we can’t find the right people in order to test, so we move to autosomal testing to help us fill in the blanks.

Autosomal Testing – For Both Sexes – The Rest of the Story

Autosomal DNA testing tests all of your 23 pairs of chromosomes that you inherit from both of your parents. You get half of each chromosome from each parent. You can see this pattern on the pedigree chart, represented by all of the 16 genealogical lines. Therefore, as you move up that tree, you should have inherited about 25% of your DNA from each grandparent, about 12.5% of your DNA from each great-grandparent, as have all of their other great-grandchildren.

Therefore beginning with your parents, you carry the following approximate amount of DNA from each of these ancestors. I say approximate, because while you do receive exactly 50% of your DNA from each parent, there is no guarantee that their parents DNA was admixed in your parents such that you receive exactly 25% from each grandparent, but it’s close. You can see the percentages in the chart below.

Generation	Relationship	% of Their DNA You Carry
1	Parents	50
2	Grandparents	25
3	Great-grandparents	12.5
4	GG-grandparents	6.25
5	GGG-grandparents	3.125
6	GGGG-grandparents	1.56
7	GGGGG-Grandparents	0.78

Given this chart, if the Native percentage is back beyond 6 generations and drops below the 1% threshold, it’s extremely difficult to discern today.

Autosomal testing will pick up relationships reliably back to about the 6^th or 7^th generations, and sporadically beyond that.

Autosomal testing provides you minimally with two things. First, with a list of “cousin matches” by percentage and estimated relationship. Second, percentages of ethnicity. It’s this second part that’s most important for the person seeking to prove Native American heritage.

Percentages of Ethnicity

As the field of genetic genealogy has moved forward, research has begun to indicate that certain autosomal markers are found in higher or lower frequencies in different ethnic populations.

For example, if someone has the Duffy Null allele, or genetic marker, we know they positively have African admixture. We don’t know how much African admixture, or from which line, or when that individual with African admixture entered their family tree, but we know for sure they existed.

Attempting to determine the population frequency of varying markers and what that means relative to other populations is the key to this analysis. Few markers are simply present or absent in populations, but are found in varying frequencies. Some populations are widely studied in the research literature, and others are virtually untouched. Thousands have only been recently discovered as part of the National Geographic, Genographic project.

The process of compiling this information in a meaningful manner so that it can be analyzed is a formidable task, as the information is often found in nearly inaccessible academic and forensic research publications. It’s difficult to determine sometimes if the DNA analysis of 29 individuals in a small village in northern Italy is, for example, representative of that village as a whole, of northern Italy, or more broadly for all of Italy. Is it representative of Italy today or Italy historically? These and other similar questions have to be answered fully before the data from autosomal testing can be useful and reliable.

Let’s take a look at all 3 of the contemporary autosomal tests and what they have to offer.

Note: as of 2019, MyHeritage is also a major player in the autosomal DNA testing space.

Family Tree DNA

Family Tree DNA sells the Family Finder test. Right now it is priced at $79 or bundled with attractive pricing with either the Y-line or mitochondrial DNA tests. I often like to use this tool in conjunction with the Y-line and mitochondrial DNA tests to see, if you match someone closely, whether you are actually related to them in a recent timeframe or if it is further back. Family Tree DNA is the only one of the autosomal testing companies that has the ability to do this type of advanced comparison. Compared to 23andMe and Geno 2.0, they are the only ones to offer traditional Y-line and mitochondrial DNA testing which provides individual marker results and matches.

In addition to a list of autosomal matches, you will receive your breakdown of ethnicity, by percent. The results below are for the same man with Native ancestry whose Geno 2.0 results are shown in the Geno 2.0 – First Peek blog.

You can read more about the Family Tree DNA autosomal product on their FAQ.

23andMe

Another company that sells autosomal testing is http://www.23andme.com. In addition to a list of cousins, you also receive admixture percentages, and their specialty, health traits. You also receive a paternal and maternal haplogroup, but with no markers for personal comparison. These Y-line and mitochondrial results are not as accurate at the Geno 2.0 nor the Family Tree DNA Y-line and mitochondrial DNA full sequence tests.

Be aware that while people who test at Family Tree DNA are interested in genealogy, the typical person at 23andMe tested for the health portion, not the genealogy portion, and may not answer contact requests or may know very little about their family history.

Right now, their test is $99, and you can download your results and upload them to Family Tree DNA for an additional $89, making the total price similar to the Family Tree DNA test. However, you need to be somewhat technically savvy to complete the download/upload process.

23andMe recently released a new version of their software which added quite a bit of resolution after years of being woefully behind. Native American wasn’t even a category previously.

Ancestry

Ancestry.com recently introduced an autosomal test. You receive matches and ethnicity percentages. However, their ethnicity percentages have significant issues and I would not recommend them at this time. Their cousin matches come with no analysis tools. So for now, just skip Ancestry and concentrate on the other resources.

One Last Autosomal Test

One marker value in particular, known as D9S919 is present in about 30% of the Native people. The value of 9 at this marker is not known to be present in any other ethnic group, so this mutation occurred after the Native people migrated across Beringia into the Americas, but long enough ago to be present in many descendants. You can test this marker individually at Family Tree DNA, which is the only lab that offers this test. If you have the value of 9 at this marker, it confirms Native heritage, but if you don’t carry 9, it does NOT disprove Native heritage. After all, many Native people don’t carry it.

To order this test, for existing Family Tree DNA clients, click on the “Order Upgrade” orange button on the right hand side of your personal page, then on “Advanced Test”, then enter “autosomal” in the drop down box, then you will see the list below. D9S919 is the last one and it costs $15. There may be a $10 one time transfer fee as well if your DNA sample is not in the Houston lab.

Swimming in Many Pools

As you can see there are lots of tools available to you that can be used individually or in conjunction with each other. Like anything else, the more work and effort you are willing to devote to the search, the more likely you are to be successful.

Most people test their Y-line and mitochondrial DNA, not just for Native ancestry, but to learn more about the lines they can test for themselves without reaching out to other family members.

Use your DNA pedigree chart to plan who to ask in your extended family to test for which lines.

Plan to test with multiple autosomal testing companies. Autosomal testing in particular is still in its infancy. I like to use the results of multiple companies, especially when you are dealing with small amounts of admixture. They use different markers, combinations, analysis tools and reference populations, so you can expect slightly different results. One company may pick up slight minority admixture while another may not. This has happened repeatedly with both my Native and African minority admixture.

GedMatch

After you obtain your results from either Family Tree DNA or 23andMe, you’ll want to download your raw data results and then upload the file to www.gedmatch.com. This is a privately run “donation” site, not associated with any of the testing companies, meaning there is no subscription or fee to use the tools, but they do appreciate and are funded by donations.

After uploading your results you can utilize several admixture tools to compare and contrast your results.

Getting Help

If you’re struggling with working through your family possibilities for who to test, I do offer a DNA Test Plan service.

If you would like a Personalized DNA Report for Y-line or mitochondrial results, those are available as well.

If you have what amounts to a quick question that I can answer in less than an hour, including prep, I offer the Quick Consult service.

For more extensive consulting, contact me. You can see my services here.

In Summary

Finding our Native ancestors is a way to pay homage to their lives and to the culture that was stripped from their descendants, ironically, by using their own DNA that has been gifted from them to us. Native people, after contact with Europeans were marginalized, and that’s the best that can be said. Many were killed, either intentionally or by European diseases, or enslaved. The results are that Native people left few if any individual records and those that might be available often can’t be identified or linked to them personally. For those who cannot unearth their Native ancestry using conventional genealogical means, genetic testing is the last hope left. Fortunately, the tools and our knowledge improve every day. We’re making great strides with what we can do, enlarging what was a pinhole into a keyhole, allowing us to peer into the past. So, click your heels, order your tests and let’s see where your DNA takes you.

______________________________________________________________

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I’m Adopted and I Don’t Know Where to Start

Posted on December 17, 2012 by Roberta Estes

This is one of the two most common querys that I receive.

I’ve addressed some of the adoptee resources in a previous blog, but in this one, I’m going to be very specific about which tests do what, what to expect, how to use them, where to purchase the tests and how much they cost in general terms. Remember when reading this, it’s meant as a guideline and you should always check current products and prices before purchasing.

We all begin with genetic genealogy to answer questions, but adoptees have a special circumstance wherein they generally know nothing at all about their birth parents. Today’s query told me that her birth certificate doesn’t even include a race.

First, all adoptees need to read my post on Adoptee Resources. I’m not an expert on how to deal with all of the bureaucratic and paperwork nightmares involved, which of course vary by state, but there are people who specialize in this and they have groups to help. Take advantage of them. Also, throughout the rest of this blog, be sure to click on the links. I’m not restating things that I’ve already covered elsewhere.

Now, let’s look at the 3 kinds of DNA testing that can benefit adoptees and just how they might use the results.

There are three kinds of DNA testing that you can do.

Mitochondrial for your direct maternal line.
Y-line for your direct paternal line – if you are a male. Sorry ladies.
Autosomal to test your ethnic mix and to find cousins related to you on any line.

On a pedigree chart, these genealogical lines look like this:

You can see the path that the Y chromosome takes down the paternal line to the brother and the path the mitochondrial DNA takes down the maternal line to both the brother and the sister. Autosomal tests the DNA of all of the 16 ancestral lines shown here, but in a different sort of way.

Let’s look at each one separately.

Y-Line DNA – For Paternal Line Testing for Males

The Y-line testing tests the Y chromosome which is passed intact from father to son with no DNA from the mother. This is the blue square on the pedigree chart. In this way, it remains the same in each generation, allowing us to compare it to others with a similar surname to see if we are from the same “Smith” family, for example, or to others with different surnames, in the case of adoption. Small mutations do take place and accumulate over time, and we depend on those so that we don’t all “look alike.”

The good news is that using comparison tools, we can determine a genetic surname in about one third of the cases. That’s pretty good odds for someone who started with no information at all.

Looking at the Estes surname project as an example, you can see in this colorized version that there are mutations shown, in color, even within family groups.

You can test at 12, 25, 37, 67 or 111 marker “locations” on the Y chromosome. In order to look for strong results you’re going to need to test at a minimum of 37 markers, preferably 67 or 111. At Family Tree DNA, which is where I recommend that you test, you can always upgrade later, but it’s less expensive in total to test more initially, plus you may well need the information to know who you match at the highest levels. Right now, 37 markers cost $119 and 67 markers are $199, but a sale is currently underway. You can also join the adoptee project to obtain the best pricing by joining a project.

Family Tree DNA also provides significant tools for Y-line DNA as well as Mitochondrial DNA as well. You can see both Family Tree and Ancestry results compared on this blog, which shows you how to use both companies’ tools. At Family Tree DNA, for all their tests, you are provided with the e-mail addresses of your matches. At Ancestry and 23andMe, you contact matches through thier internal message system. My experience has been that direct e-mails have a better response rate.

You can also order a DNA Report from my company, DNAeXplain, or directly from your personal page at Family Tree DNA, if you need assistance understanding either Y-line or mitochondrial DNA results and wringing every possible tidbit from the available tools.

Obviously, the Y-line test is only for males. Ladies, I feel your pain. However, these next tests are for both sexes.

Mitochondrial DNA – For Direct Maternal Line Testing for Both Sexes

Unfortunately, it does not follow any surname. In fact the surname changes with every generation when women marry. This makes it more challenging to work with genealogically, but certainly not impossible. Because of the surname changes in every generation, there are no “surname” projects for mitochondrial DNA, but the Mothers of Acadia project is using mitochondrial DNA to reconstruct the Acadian families.

There are three levels of testing you can take for mitochondrial DNA at Family Tree DNA, which is where I recommend that you test. The mtDNA, the mtDNAPlus and the Full Sequence. The mtDNA test is a starter test that will only leave adoptees needing more. I strongly recommend the full sequence test, but if the budget just won’t allow that, then the mtDNAPlus will do until you can afford to upgrade. Family Tree DNA is the only major lab that tests the full sequence region, plus, they have the largest matching data base in the industry.

To put this in perspective for you, the mtDNA and the mtDNAPlus tests both test about 10% of your mitochondrial DNA and the full sequence test tests all of your 16,569 mitochondrial locations. You can then compare them with other people who have taken any of those 3 tests. For adoptees, you’ll need the power of the full sequence test. Pricing for the mtDNAPlus is currently $139 and the full sequence is $199.

Update: Please note that as of 2019, Family Tree DNA is the only company providing mitochondrial DNA testing and matching. The rest are now obsolete.

If you match someone on either the Y-line or mitochondrial DNA, you may want to do some additional testing to see if you are closely related or if you are related back in time many generations. The good news is that autosomal testing is what you need and there are three autosomal pools to swim in, increasing your chances of a “hit.”

Autosomal Testing – The Rest of the Story – For Both Sexes

If there was a DNA test created for adoptees, this is it. This test can be used alone or in conjunction with the Y-line or mitochondrial DNA testing at Family Tree DNA. They are the only lab to have this advanced matching capability.

So, if you were to take an autosomal test, and another one of your grandparents grandchildren tested, you would match them at some predictable percentage of your DNA. You can see the “cheat-sheet” we use below, courtesy of the ISOGG wiki.

You can see that your grandparents other grandchildren are your first cousins, and you share approximately 12.5% of your autosomal DNA with them. Therefore, if you match someone at 12.5%, you are either first cousins, great-grandchildren/great-grandparents or another relative with 12.5 in their “box” below, as compared to you.

For an adoptee, this is the literal Holy Grail. You can match someone at the 25% level, or even the 50% level. Yes, siblings have found each other this way, although not to misset your expectations, it’s rare. Much more common are matches at smaller percentages, but even so, if you match someone who is cooperative, it’s not too difficult to work with their pedigree chart to get some idea who your parents might be. And even if you can’t figure that out, you know you are biologically related to them, something most adoptees have never experienced before aside from their own children.

The adoptee group and others are working on tools and standard procedures for adoptees, as there are ways to work with this information. I have also blogged about the basics of what autosomal DNA gives you, and how to use it.

There are three testing companies that sell autosomal DNA testing. I strongly suggest that you use all three of them, plus download your results to www.gedmatch.com and learn to use those tools, or work with someone on your behalf.

Family Tree DNA sells the Family Finder test. Right now it is priced at $199 or bundled with attractive pricing with either the Y-line or mitochondrial DNA tests. For adoptees, I often like to use this tool in conjunction with the Y-line and mitochondrial DNA tests to see, if you match someone closely, whether you are actually related to them in a recent timeframe or if it is further back. Autosomal testing will pick up relationships reliably back to about the 6^th or 7^th generations, and sporadically beyond that. In addition to a list of matches, you will receive your breakdown of ethnicity, by percent. The admixture portions are improving, but just use them as a guideline, especially for percentages below 10%, and that goes for all three companies, in general.

Another company that sells autosomal testing is www.23andme.com. In addition to a list of cousins, you also receive admixture percentages, and their specialty, health traits. For adoptees, this may be particularly important as well. Be aware that while people who test at Family Tree DNA are interested in genealogy, the typical person at 23andMe tested for the health portion, not the genealogy portion, and may not answer contact requests or may know very little about their family history. However, that doesn’t negate the possibility that you may find a very close match and you’ll never know if you don’t test. Right now, their test is $99, and you can download your results and upload them to Family Tree DNA for an additional $89, making the total price similar to the Family Tree DNA test. However, you need to be somewhat technically savvy to complete the download/upload process.

The third company is www.ancestry.com. Compared to either Family Tree DNA or 23andMe, their tools are sorely lacking, but they too offer a list of matches and ethnicity. I suggest that you simply ignore their ethnicity calculations at this point in time as they are quite misleading. The good news about Ancestry subscribers, which is who you’ll be matching, is that they too are quite interested in genealogy. Unfortunately, you don’t have the data tools you’ll need to see how you match. Again, that does not negate the importance of a close match, so I recommend fishing in this pool even though it certainly doesn’t stand up to either of the other two companies. Their price fluctuates but is floating someplace around $129. Also be aware to access the full feature set of matches including trees, you will need to subscribe to Ancestry as well in some capacity, so the test price is not the only cost involved. Be sure to read their fine print first.

After you obtain your results from either Family Tree DNA or 23andMe, you’ll want to download your raw data results and then upload the file to www.gedmatch.com. This is “donation” site, meaning there is no subscription or fee to use the tools, but they do appreciate donations. Ancestry does not provide your raw data, but has stated that they will sometime in 2013.

While this suite of tools does not replace that missing information locked away in a file someplace, or worse, it does provide adoptees with hope where none may have existed before. Various kinds of DNA testing can provide answers, and relatives, both close and distant. You can also work with these tools with other adoptees and those who specialize in genetic genealogy to unlock those doors.

Remember, the longest journey begins with a single step. Bon Voyage!

______________________________________________________________

Disclosure

Thank you so much.

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New Worldview at 23andMe

Posted on December 7, 2012 by Roberta Estes

23andMe released a new version of their Ancestry Composition – and guess what – my Native Ancestry is shown for the first time. Yahoo! It was previously shown at 23andMe as Asian, and the chromosomal locations have changed somewhat as well.

23andMe has greatly improved their product offering, moving from a significantly outdated 3 step ethnicity approach, European, African and Asian, to a multi-tiered, regional platform.

Let’s take a look at what we have today.

Here’s me in my new worldview at 23andMe under the Ancestry Composition tab. The regions where I have ancestry are brightly colored.

Looking at my ethnic breakdown, shown on the right on my page, but shown below here, you can see that I’m 99.4% European, 0.5% Native American and 0.1% unassigned.

The worldwide breakdown into regions is quite interesting as well.

By highlighting any region item, above, it shows you the corresponding region on your worldview, below. Pretty cool.

They’ve updated the Chromosome View as well. Previously, my Chromosome View looked like this:

Now, it looks like this, reflecting the new regional ethnicity information.

Another setting that you can manipulate is found in the drop down box in the upper right corner. It has 3 options, standard estimate, conservative estimate and speculative. In my case, this changes the results very little, the Native moving around a bit, but the regions within Europe do change. Be sure to take a look at all of these. The drop down box is easy to miss.

One thing I do really like about this new rollout is that the X chromosome is included. You can see it at the bottom of the list. This is new and has been promised for a long time.

One feature that I would very much like to see is the ability to determine which, if any, of my matches actually match me on the segments determined to be Native American. I realize that not everyone at 23andMe is interested in genealogy, but if you could contact them and say, “Hey, we match on my Native segment – let’s see if we can find some common ancestry,” it might generate enough interest to garner a response. I would like to find a way to use these results more effectively. I think there is a lot of unrecognized potential just waiting to be harvested.

All in all, a significant step forward for 23andMe. For me, not a lot of new information. I discovered that I have some Native genes on chromosome 2 in addition to chromosome 1. My African ancestry picked up elsewhere is missing here. Fortunately, my Native American heritage is now classified as such, and not Asian. However, on the speculative view, I still have a smidgen of Asian, likely from the Native American heritage. I really like the 3 choices in how to display results, conservative, standard and speculative.

As soon as the National Geographic Geno 2.0 ethnicity information is available, I’ll be comparing all the results from the various companies against my known genealogical heritage and taking a look at all of those results combined. Stay tuned….things are really getting interesting!

______________________________________________________________

Disclosure

Thank you so much.

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