The Genetic Genealogist

As I’ve stated many, many times in the past, the future of genetic genealogy is combining test results with both family trees and paper records.

Today, MyHeritage and Family Tree DNA announced a partnership that will bring that future one step closer to reality.  MyHeritage will offer a full line of tests (13 in total) through FTDNA, including these basic introductory tests (with discounts – not shown below – for MyHeritage subscribers):

• Y-DNA12 (12 Y-STR markers) – $99
• mtDNA (HVR1 region) – $99
• Family Finder (autosomal test) – $298

The FAQ page for the tests is here (and I note that although they currently do not allow import of test results from other providers, they plan to in the future).  I wonder if existing FTDNA test-takers can import their results?

Given MyHeritage’s worldwide reach and enormous membership (62 million members around the world!), it will be interesting to see whether this new partnership expands genetic genealogy testing in other parts of the world, which have been slow to try this technology.

Today’s Press Release:

MyHeritage brings DNA testing to the global community

World’s largest family network offers DNA testing to a new global audience – enabling millions of families to discover their ethnic roots and previously unknown relatives

PROVO, Utah & LONDON & TEL AVIV, Israel – February 16, 2012: MyHeritage, the most popular family network on the web, announced today the integration of DNA testing into its core family history offering. The move adds genetic genealogy to the company’s suite of tools for researching family history, used by millions of families around the world.

With more than 62 million registered users and 21 million family trees, MyHeritage has become the trusted home on the web for families wishing to explore their family history, share memories and stay connected. With the new biological layer added to the MyHeritage experience, users can now enjoy a service combining science, intuitive web features and social networking for discovering and sharing their family legacy.

“DNA testing provides a fascinating new way to discover one’s origins and find previously unknown relatives”, said MyHeritage Founder and CEO Gilad Japhet. “Offering the highest quality DNA tests to our tens of millions of users around the world in 38 languages, and providing DNA matches with hundreds of thousands of people who have already had their DNA tested, significantly advances our mission of bringing family history to the masses. By combining DNA with our innovative Smart Matching™ technology, families will be closer than ever before to constructing a more complete picture of their history”.

DNA is the hereditary material in humans and almost all other organisms. By purchasing a simple cheek-swab DNA test, users can now use information contained in their DNA to find present-day relatives who share a common ancestor up to many hundreds of years ago. A DNA test can also reveal ethnic origins such as Native American, African or Jewish descent on paternal or maternal lines, as well as uncover ancestral information for those who were adopted.  While DNA tests can break through brick walls in family history research by revealing biological relations, MyHeritage’s flagship Smart Matching™ technology then steps in to help piece together the paper trail by uncovering how the family trees of related people actually connect. In addition, people with the same paternal surname can get together via MyHeritage to see if they’re related by DNA.

MyHeritage is introducing today a wide range of DNA tests to meet different research objectives and budgets, with special discounted prices for MyHeritage subscribers starting from as low as $84. Users can identify the deep ancestral origins of their direct paternal line (Y-DNA), of their direct maternal line (mtDNA), find relatives across all lines via autosomal DNA (Family Finder), receive a percentage breakdown of their ethnic roots and confirm or disprove whether someone is a close relative. View the full list of the DNA kits on MyHeritage and a list of Frequently Asked Questions about DNA tests on MyHeritage.

For the analysis of users’ DNA tests and the DNA matching, MyHeritage is working with long-time partner and global leader in genealogy DNA, Family Tree DNA. Pioneers of genetic genealogy and with a state-of-the-art laboratory, Family Tree DNA has established the world’s largest DNA database for genealogy and is well known for its work with National Geographic on the Genographic Project. All information is kept strictly confidential and is never shared.

Bennett Greenspan, President and CEO of Family Tree DNA said “We’re proud to work with MyHeritage to bring DNA testing to a much wider, global audience. The phenomenal size and reach of the global MyHeritage family network will create new horizons in collecting DNA data, helping many more people discover their ancestral origins”.

About MyHeritage

MyHeritage is the most popular family network on the web. Millions of families around the world enjoy having a private and free place for their families to keep in touch and to showcase their roots. MyHeritage’s Smart Matching™ technology empowers users with an exciting and innovative way to find relatives and explore their family history. Following the November 2011 acquisition of FamilyLink in Provo, Utah, MyHeritage offers billions of historical records through its website WorldVitalRecords.com. With all family information stored in a secure site, MyHeritage is the ideal place to share family photos and preserve special family memories. The site is available in 38 languages. So far more than 62 million people have signed up to MyHeritage. The company is backed by Accel Partners and Index Ventures, the investors of Facebook and Skype. For more information visit www.myheritage.com

Press Contact

Daniel Horowitz                                   Schelly Talalay Dardashti                   Mark Olsen

Chief Genealogist                               US Genealogy Advisor                       Affiliate Manager

MyHeritage.com                                 MyHeritage.com                                 MyHeritage.com

Daniel@MyHeritage.com                   (505) 994.1554                                    (801) 687.0599

Direct-to-consumer DNA testing has led to the re-joining of yet another family.

Y-DNA and autosomal testing by Family Tree DNA has revealed that two NFL players , Xavier Omon (San Francisco 49ers)) and Ogemdi Nwagbuo (San Diego Chargers), are half-brothers.  ESPN has a long write-up of the story at “A brothers’ tale for Omon, Nwagbuo.”

Meeting for the First Time

The brothers had planned to meet face-to-face yesterday, September 1, 2011, as their teams met on the field.  Turns out Omon’s team, the 49ers, were victorious, meaning that if he’s anything like my brothers, he gave Nwagbuo a hard time about it!  The Mercury News has a story about the brothers’ first meeting at “Omon meets half-brother (a Charger) for first time,” and the SF Gate has a story at “49ers’ Xavier Omon meets half-brother.”

Family Tree DNA’s Press Release:

Houston, TX – August 31,2011 – Family Tree DNA, the pioneer and largest DNA testing company for genealogy purposes, through its Family Finder test, provided the conclusive proof that two NFL players are half-siblings.

Until a few months ago, Xavier Omon, from the San Francisco 49ers and Ogemdi Nwagbuo from the San Diego Chargers did not have a clue that they were related. Early August, at the request of ESPN, Family Tree DNA performed the Family Finder test on both, and the result was unequivocal: definitely half-siblings. More of the story can be found at the ESPN website,under the “Brother’s Tale” story.

The Family Finder test allows connecting with family members across all ancestral lines. While the Y-DNA matches men with a specific paternal line and the mtDNA finds potential relatives only along the maternal line, Family Finder can look for close relationships along all ancestral lines. Anyone, regardless of their gender, may confidently match to male and female cousins from any of their family lines in the past five generations. The science is based on linked blocks of DNA across the 22 autosomal chromosomes that are matched between two people. Based on this concept, Family Tree DNA bioinformatics team has worked extensively to develop the calculations that would yield the closeness of the relationship. The possibilities to find matches abound: grandparents, aunts and uncles; half siblings; first, second, third and fourth cousins; and, more tentatively, fifth cousins.

About Family Tree DNA

Founded in April 2000, Family Tree DNA was the first company to develop the commercial application of DNA testing for genealogical purposes, something that had previously been available only for academic and scientific research. Almost a decade later, the Houston-based company has a database with over 345,000 individual records – the largest DNA database in genetic genealogy, and a number that makes Family Tree DNA the prime source for anyone researching recent and distant family ties. In 2006 Family Tree DNA established a state of the art Genomics Research Center at its headquarters in Houston, Texas, where it currently performs R&D and processes over 200 advanced types of DNA tests for its customers.

Media contact

Sharon Weisz, —tel: 323-934-2700; e-mail: Sharon@familytreedna.com

As you may have heard, I recently made my 23andMe and Family Tree DNA autosomal testing results available for download online at “mygenotype,” and dedicated the information to the public domain (if dedicating DNA sequence to the public domain is even possible – I’m currently doing some research in this area and expect to write more in the future).

At “mygenotype” you can download the following:

My Family Tree DNA Results:

1. Affymetrix Autosomal DNA Results (2010)
2. Affymetrix X-Chromosome DNA Results (2010)
3. Illumina Autosomal DNA Results (2011)
4. Illumina X-Chromosome DNA Results (2011)

My 23andMe Results:

1. V2 Results (2008)
2. V3 Results (2010)
3. Y-DNA Results (2010)
4. mtDNA Results (2010)

You can also find my SNPedia Promethease reports:

• Promethease Report using an early version of Affymetrix Family Finder DNA Results

• Promethease Report using V2 23andMe DNA Results

• Promethease Report using pooled 23andMe and Family Finder DNA Results

In addition to my genome, Razib Khan of Gene Expression has a spreadsheet of approximately 48 other genomes that are available for download online.

A Challenge To YOU

Now that the information is out there, available to anyone who might be interested, it remains to be seen who might be interested in the information.

Indeed, as evidenced by Razib’s spreadsheet, while dedicating a genome to the public domain has only been done by a small handful of people worldwide, it isn’t as novel as it was just a few months ago.

So, I’m challenging everyone who reads this to download my data and analyze it to find the most interesting or surprising results.  For example, you could use my most recent 23andMe V3 data.

I’ve already done a fair amount of analysis myself, including the Promethease reports above (and see here), and a recent blog post about my vastly increased Type 2 Diabetes risk.  However, perhaps there’s a recent but relatively study that applies, or perhaps there’s a story you can weave with a handful of SNPs. Or, even better, what can you tell me about my ancestry other than mtDNA and Y-DNA haplogroups? Don’t worry about the strength of the study, reproducibility, etc. – I’m aware of the uncertainties associated with this type of research, and my goal here is to make people aware of possibilities.

Please post your findings in the comments below, and in two weeks I’ll pick the most surprising or interesting findings and make them the focus of a new blog post.

Can you surprise me with my own genome?

DNA Heritage, a popular genetic genealogy company intiated in 2002, has ceased operations (although pending orders will be fulfilled).  The company’s website announced today that it is in the process of transferring their database and domains to Family Tree DNA.

Family Tree DNA, meanwhile, has announced that it records in the DNA Heritage database will only be placed into FTDNA’s database if the owner agrees to opt-in.  FTDNA has a series of FAQs related to the transfer available here.

The full text of the announcement is below:

As of April 19 2011, DNA Heritage has ceased its operations and is in the process of transferring the domains DNAHeritage.com and Ybase.org to Family Tree DNA.

All the tests in progress will be processed by our current lab and the results will be delivered to our customers.

In order to ensure the continuity of the existing surname projects Family Tree DNA will study the best options to integrate our customers’ results into their database. Once Family Tree DNA decides on the option(s), our customers will be given the opportunity to opt-in to their database.

If you have questions about the transition or need to place an order please check: http://www.familytreedna.com/landing/dna-heritage.aspx

Last week I wrote about the results of my Family Finder autosomal DNA test by Family Tree DNA (see “A Review of Family Tree DNA’s Family Finder – Part I“).  The Family Finder test uses a whole-genome SNP scan to find stretches of DNA shared by two individuals, thus identifying your genetic cousins (and will soon include the Population Finder analysis of admixture percentages).  I currently have over 33 genetic cousins in Family Finder, and I’m working with them to identify our common ancestor(s).

The Affymetrix microarray chip used by FTDNA includes over 500,000 pairs of SNPs located on the X chromosome and the autosomes (no Y chromosome SNPs).  Via SNPedia:

FamilyTreeDNA uses an Affymetrix Axiom CEU microarray chip with 3,269 SNPs removed (563,800 SNPs reported) for autosomal and X (but not Y or mitochondrial) ancestry testing for $289. Other sources have cited 548011 snps. This platform tests 1871 of the 12442 snps in SNPedia.

FTDNA states that the Family Finder test is not intended to be medical.  From the FTDNA FAQ:

Question: Is the Family Finder test medical?

Answer: No, it is not.

This is entirely accurate of course; FTDNA does not analyze the test results for health, traits, or other medically-relevant information, and does not provide the user with any medical information or analysis tools that might reveal medical information.

However, when DNA is involved there is almost never any such thing as a completely non-medical test.  It’s often impossible, at any given point in time, to know which of an individual’s SNPs might be affiliated – remotely or closely – with a medical state or condition.  Ann Turner recently wrote the following at the Rootsweb GENEALOGY-DNA mailing list in response to another individual’s question:

Question:  “I am wondering if FTDNA really left out the genes and just lists the intergenic areas?”  Answer:  “No, the claim was that they scrubbed medically significant SNPs.  They still include over 1600 SNPs with entries in SNPedia, which would have some phenotype implications, according to an analysis posted at DNA-Forums: http://tinyurl.com/27slbj8.”

Indeed, as of August 3rd, 2010, there are 12,442 SNPs in SNPedia, of which a total of 1,871 are tested by Family Tree DNA’s Family Finder test.

Promethease Analysis

I was curious as to what information my Family Finder results might contain, so I ran my results through Promethease, a free software tool used to analyze whole-genome SNP scan results.  From the Promethease website:

“Promethease is a tool to build a report based on SNPedia [an impressive database of annotated SNPs] and a file of genotypes [i.e., your Family Finder results]. Customers of testing services (23andMe, deCODEme, Navigenics, …) can use it to learn more about their DNA. It can also pool the data from multiple testing services. The program runs for approximately 3 hours. An optional $2 payment per run unlocks extra features and reduces runtime to approximately 5 minutes.”

Similar to several of the other autosomal SNP scan testing companies, Family Tree DNA allows the customer to download their own DNA testing results.  Autosomal results and X-chromosome results are separately downloaded as compressed files which can then be extracted for analysis.  After downloading and installing Promethease, I ran the program using just my Family Finder results (after paying the $2 for a faster runtime.  I’m impatient.).

Promethease was  indeed able to analyze my Family Finder results and returned a report that included 1881 annotated genotypes. Here, for example, is a screenshot from my results (click to embiggen):

In addition to the “most interesting snps” category, there are categories for “medicines”, “medical conditions” (below), and others.  After clicking on “more” for each category, I receive more information about those annotated SNPs.  To get an idea of what the full results look like, there are a number of people who have shared their real promethease reports.

Promethease also lets you upload your results from different companies, so I also analyzed my Family Finder results together with the results of my 23andMe test.  Since there isn’t much overlap between the SNPs in the FTDNA test and the SNPs in the 23andMe test (see this ISOGG Wiki page for more information about FTDNA’s testing versus 23andMe’s testing, for example), I was able to extract information about 7691 of my personal genotypes using the SNPedia database (compared to 1881 genotypes with my Family Finder results alone).  Thus it appears that the 23andMe results are more likely to contain SNPs that are annotated in SNPedia.  This isn’t surprising considering that, according to reports, FTDNA designed their chip to contain fewer annotated SNPs.

My Results

Since I have taken whole-genome tests before and was familiar with both testing and the interpretation of results, my report was not surprising.  Indeed, I was already aware of my increased risk of type-2 diabetes (see Personalized Genomics: A Very Personal Post ), as well as the fact that I’m “probably light-skinned” (see e.g., my bathroom mirror).  However, it might not be clear to those taking these tests that the results contain a large amount of medically-relevant information.  This can be problematic when considering the fact that Family Finder test-takers might share or reveal their data with other people.  Indeed, even knowledge that you share a region of DNA with another person can reveal medically-relevant information that the two people share in that region.

On the other hand, this ability to apply Family Finder results to information in SNPedia will be of great interest to a number of test-takers who are interested in this type of genetic analysis.  This type of “do-it-yourself biology” is becoming more and more popular everyday.  Although there is still much debate regarding the utility of such information, exploring one’s genome can be highly interesting, informative, and interesting (and, to date, no one has adequately shown that exploring one’s genetic data is harmful for anything other than a tiny minority of people).

Conclusions

In conclusion, it is important for consumers to realize that ALL genomic information has the potential to reveal medically-relevant information (even Y-DNA and mtDNA results can include health information, for example).  By no means, however, am I suggesting that people should forgo whole-genome SNP scans, or that governmental regulation is needed.  Instead, I think it is vital that consumers understand the testing process and possible outcomes before testing, and I fully believe that it is the consumer, not the government, who should decided whether the consumer should or can undergo testing.

Indeed, rather than expend thousands of dollars in hearings, [faulty] investigations, and regulation, the government could use that money to fund programs that educate the population about genetics and DTC testing.  After all, we are entering a future that will involve our personal genomes in many aspects of our lives.

I’m interested to hear your thoughts on this subject, so please feel free to leave a comment below.

(Disclaimer: Please note that I received my Family Finder test without charge from Family Tree DNA for purposes of this review.  Regardless, I have attempted to review this product as honestly and as objectively as possible in order to provide valuable information about Family Finder to my readers.  I am also a consultant for Pathway Genomics.)

Since late 2007, several “direct-to-consumer” or “DTC” genetic testing products have entered the marketplace, many of which offered some degree of autosomal ancestry analysis (including 23andMe, deCODEme, and Pathway Genomics, among others).

In early 2010, genetic ancestry testing company Family Tree DNA announced that it would begin offering a new genetic genealogy product (see “Announcing Family Finder – An Autosomal Test From Family Tree DNA”).  The new product, called “Family Finder,” is one of only a very few autosomal genetic genealogy tests available to consumers.

The Family Finder test uses an Affymetrix microarray chip that includes over 500,000 pairs of locations called single nucleotide polymorphisms (SNPs) in your autosomal DNA.  Once the SNPs are analyzed, FTDNA detects linked blocks of DNA that indicate a common ancestor.  The number and size of these linked blocks is used to determine how recently or closely two people are related.  From the Family Finder FAQ page:

“The Family Finder test works by comparing your autosomal DNA to that of other people in our database who have taken the test. Your relationship with a match is calculated based on sharing linked segments of DNA. Although any two people from the same population may have some of their DNA in common, as a matching segment of DNA becomes longer and you share more segments, it becomes more likely that the sharing is due to a recent common ancestor than a chance match.”

Thus, the results of the Family Finder test are used to find stretches of DNA shared by two individuals, to identify your “genetic cousins” (as compared with “genealogical cousins,” who you may or may not share DNA with).

The Family Finder landing page is packed with information, including videos and information about the potential uses of the product:

“We place you in control. When you take the Family Finder test, your results are compared against our Family Finder database. Your list of matches is designed to be quickly sorted to allow you to focus on your near or distant cousins. Because email addresses are provided for easy communication with your near or distant cousins you will be able to share research easily. We notify you by email when you have new matches. Your raw data file is freely available for download.”

Frequently Asked Questions Page

The Family Finder FAQ page is especially well-developed for such an early stage product.  There are currently over 75 FAQs including a wide range of questions and answers, including the following:

Question: What is the probability that my relative and I share enough DNA to be detected by Family Finder?

Answer: If you are related within five generations (3^rd or more recent cousins) then Family Finder is almost sure to detect your relationship. Testing will also detect many 4^th and 5^th cousins and a small percentage of more distant cousins.  Chances of finding a match if the relationship is:

Connecting with Cousins:

Unlike 23andMe’s Relative Finder, where communicating with genetic relatives in their database can be challenging (although 23andMe is launching improvements to the system that will make identifying and communicating with relatives easier), this product is intended for and marketed to genealogists.   The results are provided using the following format (picture courtesy of the ISOGG wiki Family Finder page, image has been altered for privacy reasons):

The results provide information about the identified genetic cousin, including the suggested relationship, the predicted relationship range, the shared cM (centimorgans), the longest block of shared DNA, and the ancestral surnames that the user has provided in their profile (if any).  Also provided is a link to the user’s email address to facilitate communication.

As a result, there are several privacy issues involved in the Family Finder test that test-takers should be aware of.  It is important to recognize that your name and the email address you sign up with will be made available to your genetic relatives.  For most genealogists this is a welcome development, but it is worth highlighting.  Additionally, if you share closely-matching DNA with an individual, that individual will see your name in their results and can share that information with other people.  Although ethically all test-takers should always keep these privacy issues in mind, there is nothing to prevent them from sharing the information.  Please be informed before you order this test.

Chromosome Browser:

Family Finder also provides a Chromosome Browser which test-takers can use to explore and compare the blocks of DNA that they share with genetic cousins.  Users can compare the blocks of up to 3 people, and can filter blocks from 10+ cM, 5+ cM, 3+ cM, down to 1+ cM.  Users can also view the comparison information in a table and download it to an Excel file.

Download of Results

Like 23andMe, Family Tree DNA offers customers the ability to download the results of the SNP test.  The autosomal results and X-chromosome results are offered in separate zipped files.

My Results:

I currently have 33 genetic relatives in the Family Finder database with the following break-down:

• Only one person with a suggested relationship (my closest relative in the database), suggested at the 4th cousin stage, with a range of 3rd to 5th cousin;
• Eight cousins at the 4th cousin to distant cousin stage; and
• 24 cousins at the 5th cousin to distant cousin stage.

I am communicating with my matches in order to identify a shared ancestor in our respective trees.   In the one instance where we’ve identified shared ancestry, we share relatives in a minimum of twelve different lines (via the early colonial era).  I’ve also matched several relatives from an isolated geographic region where I have confirmed recent ancestors, although we have not yet identified a common ancestor.

Future Developments

Ancestral Percentages

At the current time, the Family Finder test results do not include information about possible ethnicity or biogeographical ancestry.  However, it appears that Family Tree DNA plans to offer this type of information in the future.  See, for example, “Relative Finder vs. Family Finder” at The Melungeon Historical Society blog.  There Roberta Estes writes the following:

“Family Tree DNA does not initially offer the percentages of ethnicity, but that will be added shortly. The 23andMe ethnicity percentages (European, African and Asian) are very, very conservative and I believe so conservative as to be significantly incorrect. Suffice it to say that I have been involved with the new ethnicity percentage information and presentation at Family Tree DNA, and it will blow the socks off of anything out there today.”

23andMe Results at FTDNA

What if you’ve already tested at 23andMe?  Once again, Roberta Estes writes the following (which includes information I’ve seen at several other places):

Family Tree DNA will (shortly) facilitate an upload of 23andMe raw data for a $40 and they will then compare the 180,000 (280,000 by inference) common locations between their data base participants and your 23andMe data. If you later decide to take the Family Finder FtDNA test, they will credit your $40 to that test. Only the people who ordered the full health traits and ancestry version of the 23andMe product can gain access to their raw data at 23andme. Everyone who participated in the beta can download their raw data.”

Experiences and More Information:

Family Finder Links:

• Worldfamilies.net has a Family Finder page with information about the product.
• Kimberly’s Genealogy Blog writes “FamilyTreeDNA vs. 23andme – A First Look”
• The Family Finder page at the ISOGG wiki (a great new resource, by the way)
• The FamilyTreeDNA page at SNPedia

Conclusions

I first had part of my genome sequenced over 7 years ago via an AncestryByDNA test.  Since then I’ve had mtDNA sequencing, Y-DNA sequencing, SNP scans, and a number of other tests performed.  Accordingly, I consider myself to be an early explorer in the field of DTC genetic testing.  I enjoy learning about my genetic ancestry, about genetic cousins, and about my own genome.  Many of the other early adopters of the Family Finder test are also pioneers.  I would recommend this test to anyone who is interested in their genetic ancestry, or anyone that is interested in learning more about their own genetic heritage.

One of the best things about the Family Finder test is that it gives the user information and then allows them to use that information as they so choose.  Although the test does reveal your name and email address to genetic relatives, it is up to you whether you reply to requests or explore those relationships.  Family Finder is yet another tool that allows personal genome explorers to learn about themselves.

Have you used FTDNA’s Family Finder test?  I’d love to hear about your experiences in the comments section.

More Soon…

Stay tuned, in the next week or so I’ll be posting more of my review of Family Tree DNA’s Family Finder, including some advanced tools for Family Finder and/or 23andMe users .

Disclosures

I received my Family Finder test without charge from Family Tree DNA for purposes of this review.  Regardless, I have attempted to review this product as honestly and as objectively as possible in order to provide valuable information about Family Finder to my readers.  I am also a consultant for Pathway Genomics.

On May 6, 2010, the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany presented the world with a draft of the genome sequence of the Neanderthal (press release here (pdf) and full article here (free), NYT article here).  As part of the announcement, the team presented their conclusion that 1% to 4% of the genome of non-Africans is derived from Neanderthals:

“An initial comparison of the two sequences has brought some exciting discoveries to light. Contrary to the assumption of many researchers, it would appear that some Neandertals and early modern humans interbred. According to the researchers’ calculations, between one and four percent of the DNA of many humans living today originate from the Neandertal. ‘Those of us who live outside Africa carry a little Neandertal DNA in us,’ says Svante Pääbo.  Previous tests carried out on the DNA of Neandertal mitochondria, which represents just a tiny part of the whole genome, had not found any evidence of such interbreeding or ‘admixture.’”

Once this study came out, I knew it was only a matter of time before companies began offering tests that examined the percent of Neanderthal contribution to a test-taker’s genome.

The Neanderthal Index

In May 2010, DNA Consultants began offering a test called the Neanderthal Index.  Priced at USD $90.00, the test purports to “estimate how much Neanderthal is in your ancestry.”  From the test description:

“Created in response to the phenomenal interest generated by the revelation in scientific journals on May 8, 2010 that most humans are part Neanderthal (Green et al), our autosomal DNA Neanderthal Index can be added to your DNA Fingerprint Test or DNA Fingerprint Plus. It reports any strong matches you have with populations identified as Archaic, those preserving the earliest earmarks of interbreeding between Neanderthals and humans (Homo sapiens sapiens). The stronger the match the higher the likelihood that your ancestors gave you Neanderthal genes.”

The site also provides an FAQ page, and a sample test result (pdf).  The test returns results on a scale of 0.1 to 5.0, but it is unclear if this is meant to be a percentage.

It is vital to understand that this test does NOT test SNPs.  Instead, it uses CODIS markers to estimate whether a test-taker’s results are likely to be found in “archaic populations,” which themselves are hypothesized to be more likely to possess Neanderthal DNA (i.e., “relatively little genetic inflow.”).  The list of archaic populations is found in the FAQ, and includes many Middle Eastern and worldwide indigenous populations.  From the test description:

“Note that this test does not directly examine your genetic material. Only a large-scale genomic sequencing procedure like the Human Genome Project or Draft Neanderthal Genome can do that. The Neanderthal Index is based on probabilistic predictions of the occurrence of your unique DNA Fingerprint in Archaic Populations retaining Neanderthal genomics and traits.”

While the website does a good job of explaining that it does not identify any specific “Neanderthal SNPs” but rather makes a incredibly rough probabilistic estimate based on the Science paper, it is important to fully understand the many limitations of this test.

DIY Genomics

Meanwhile, over at 23andMe, several test-takers refuse to wait for commercial companies to offer Neanderthal-specific testing.  In addition to asking in the 23andMe forums when the Ancestry Painting will include the percentage of Neanderthal DNA, others have proposed several so-called “Neanderthal SNPs” based on research published in other recent papers.  These SNPs include rs1864325 (forum discussion here) and rs930557 (forum discussion here).   This collaborative effort by 23andMe’s test-takers is just one of the many reasons that personal genomics and affordable sequencing are so exciting.

Although the science behind these Neanderthal SNPs is only in its infancy and should only be taken with an enormous grain of salt at this stage, there will be more of these types of studies in the future to provide companies and pioneers with new data to explore.  And we, the personal genome pioneers, will get to learn and explore as these developments unfold.

Conclusions

While there aren’t yet any commercially-available tests that examine your genome for evidence of Neanderthal contribution, there will undoubtedly be such tests in the next few years, especially as further drafts of the Neanderthal genome are released.

The following is a press release from GeneTree:

New GeneTree Services Enable Users to Make Sense of Genetic, Genealogy Information

• New GeneTree Products and Services Focus on Making Genetic, Family History Information Comprehensible and Meaningful to Users
• As a wholly owned subsidiary of Sorenson Molecular Genealogy Foundation, GeneTree is able to Leverage the World’s Most Comprehensive Collection of Correlated Genetic and Genealogical Information on Behalf of Users
• Re-Designed Web Site Includes Enhanced Content and Features

SALT LAKE CITY (March 31, 2010) – GeneTree today announced that the company has launched a new product offering of integrated genetic and genealogical services unique in the marketplace for its ability to expand users’ knowledge of their genetic and family history connections. The company also announced it has significantly revamped its Web site, www.genetree.com.

GeneTree’s comprehensive new service offering focuses on integrating two essential sources of human identity: quality genetic tests and industry-standard family history consulting services. In contrast to providers that focus exclusively on anthropological deep ancestry, GeneTree’s product and service offering is designed to help people discover near-term family connections in the last six to ten generations as well as deep ancestral connections.

The company has developed a diverse array of genetic and genealogical consultation services to provide users with a rich sense of their family trees. These services range from providing instruction and support for people who want to make sense of their own research, to comprehensive services for those who prefer that GeneTree conduct research for them. GeneTree’s highly qualified, professional genetic genealogists provide individualized assistance about users’ family trees and how DNA results can help them in their search for connections.

Genetic information informs family history efforts in two primary ways. First, it helps to ensure the accuracy of the genealogical record, by validating family connections and identifying potential errors. Second, genetic analysis expands the universe of connections available to individuals and families for whom written genealogical records have hit a dead end.

GeneTree helped Lueda Thomas of Omaha, Neb., affirm the identity of her ancestor Josiah Sims, correct inconsistencies in two pedigree charts she was studying, and expand her family tree. “I have spent seven years trying to link Josiah Sims into another pedigree chart,” said Thomas. However, there was a 10-year discrepancy between the birth dates attributed to Sims on the two respective pedigree charts, though each reported the same name.

Thomas found two potential living relatives and worked with GeneTree to obtain DNA tests for each of them. Both tests yielded a perfect match and confirmed that the Josiah Sims on both of the pedigree charts she was studying were in fact the same person. In addition, a search in GeneTree’s database revealed another perfect match, providing Thomas with a third newly discovered living family member. “I had exhausted all of my resources and knew that DNA was the only way I could find an absolute answer to this question,” said Thomas.

GeneTree offers a series of DNA tests that can be tailored to the goals of users ranging from individuals to major family history research projects. The company’s genetic testing services, certified by the National Institute of Standards and Technology (NIST), include both Y-DNA (genetic information passed from fathers to sons) and mitochondrial (mtDNA; genetic information passed from mothers to all their children). GeneTree customers can use their DNA results to verify and significantly expand their family trees.

GeneTree’s revamped Web site features a complete redesign, together with practical insight about DNA testing and genealogy. A revised shopping cart contains products and services that enable users to take advantage of the synergies between genetic and genealogical information. In addition, GeneTree’s dynamic DNAvigator online map allows users to trace the geographic connections and migration patterns of their genetic ancestral groups.

“The popularity of shows like Who Do You Think You Are? demonstrate that there is a genuine hunger for people to know who they are fundamentally-what is their genetic legacy and how they fit into the larger family history picture,” said Jeff Wells, CEO of Genetree. “GeneTree is uniquely qualified to help people answer these questions.”

GeneTree clients will also benefit from the relationship with its parent, the non-profit Sorenson Molecular Genealogy Foundation (SMGF), which has developed the world’s largest and most comprehensive collection of genetic information correlated with multi-generational genealogical family pedigrees.

“Our relationship with SMGF enables GeneTree to combine sophisticated DNA analysis with traditional genealogical research to provide our customers with the most complete picture of human identity available anywhere in the world,” said Wells. “The extensive, complementary insights GeneTree customers can obtain through this process are without parallel in making genetic and family history information understandable and useful.”

About GeneTree

GeneTree (www.genetree.com) is the leading provider of genetic and family history services that unlock people’s ancestral legacy. Powered by the world’s largest, most comprehensive repository of genetic and genealogical information, GeneTree’s best-in-class genetic testing, genetic genealogy consulting and family history research enable individuals and extended families alike to dramatically extend their family trees.

Randy Seaver at Genea-Musings (“I’m Puzzled by DNA Claims on ‘Faces of America’”) writes about the fourth and last episode of “Faces of America,” a PBS documentary series investigating the ancestry of several famous people in America. This fourth episode included several different types of genetic genealogy to examine the ancestral origins and relatedness of the show’s members.

1. Whole Genome Sequencing by Knome

The first type of genetic genealogy was whole-genome sequencing by Knome of Henry Louis Gates and his father. This analysis examined Henry’s (“Skip’s”) genome for medical conditions and physical traits, and also compared his DNA to his father’s, thereby allowing them to deduce the entire DNA contribution from his deceased mother. This segment was actually quite moving, as Dr. Gates was able to establish this intimate connection to the mother that he and his father obviously missed very much.

2. SNP Analysis by 23andMe

The second type of analysis was large-scale SNP analysis of everyone’s genome by 23andMe. The show primarily focused on the Ancestry Painting, which uses information from throughout the entire genome to determine a very rough estimate of your ancestry. Ancestry Painting breaks down the genome into three categories: Asian/Native American, European, and African. Stephen Colbert, for example, was 100% European, while Eva Longoria was 70% European, 27% Asian/indigenous, and 3% African. I don’t recall any mention or use of 23andMe’s medical or physical trait analysis in the show.

3. mtDNA and Y-DNA Haplogroups

The third type of genetic genealogy was haplogroup testing. In this segment, Dr. Gates spoke with Dr. Bryan Sykes of Oxford Ancestors, which was interesting because it was the first time I’ve ever seen him speak. There didn’t appear to be any surprises here.

4. Mysterious Genomic Comparisons

The fourth type of genetic genealogy testing in the episode is what has caused so much confusion among genealogists. Dr. Gates introduced David Altschuler and Mark Daily as “research geneticists at the Broad Institute.” According to Dr. Gates, Altschuler and Daily have “pioneered a new kind of genetic analysis that can determine if any two people share a common ancestor within the last several centuries.” Although Dr. Gates repeatedly said within the last “250 years”, the scientists repeatedly said “hundreds of years.” A slight difference perhaps, but I tended to disregard the “250 years” as more of a simplification by Gates for purposes of the show rather than any actual limit discussed by the scientists. Regardless, this doesn’t make their analysis any more clear.

Unfortunately, I have been unable to locate any discussion, literature, or publication by Altschuler or Daily (or anyone else) discussing this “new kind” of genetic analysis. If you’re familiar with one, please point it out in the comments so that we can understand their analysis.

Interestingly, the members of the series apparently did not match each other in 23andMe’s Family Finder, since the 23andMe system would have picked up on that, and further analysis would not have been necessary. And since it appeared that they did NOT undergo further testing, I imagine they used their 23andMe data for the analysis by Altschuler and Daily.

As an example of this comparison, according to Altschuler and Daily, Yo-Yo Ma (who was 100% Asian in his 23andMe Ancestry Painting) is related to Eva Longoria (who was 70% European, 27% Asian/indigenous, and 3% African) within the last few centuries. It obviously wasn’t through Native American DNA since any connection there was many, many thousands of years ago. Does Longoria have more recent Asian DNA perhaps? It seems unlikely (but is certainly not impossible). The fact that this was simply glossed over was an oversight.

I’m having a hard time understanding the results from Altschuler and Daily.  Can anyone else shed any light on their analysis?

Conclusion

Despite the confusion created by the fourth type of genetic analysis, I really enjoyed this episode of Faces of America. As always, it was interesting and entertaining to watch them receive their results and explore their ancestry.

What are your thoughts?

Kevin Davies, Ph.D., currently the Editor-in-Chief of Bio-IT World, recently wrote an article about Pathway Genomics in which he reviewed the company’s Health Test product (see “Pathway and Me: Consumer Genomics Firm Delivers First Results”):

“Earlier this year, I submitted a saliva sample to Pathway to get a feel for how the latest consumer genomics offering compares to the more established companies in the field. Pathway communicates the health results not by a numerical relative or lifetime risk but via a series of color-coded bins depending on their potential significance to the individual.”

I too recently had the opportunity to test my DNA through Pathway Genomics. (DISCLAIMER: Although this test kit was not free, I am a consultant for Pathway Genomics. This review, however, contains my own opinions of the Pathway Genomics Ancestry Test product). This is a brief review of the Pathway Genomics Ancestry Test, which examines SNPs on the mtDNA (for both males and females) and the Y-chromosome (for males). Using those results, Pathway classifies test-takers into one of over 1,200 maternal haplogroups and one of over 525 paternal haplogroups.

mtDNA Results

Based on my SNP results, Pathway classified me as belonging to maternal haplogroup A2, a predominately Native American haplogroup:

It was actually a major victory for Pathway to classify me as A2. Although I already knew that I’m haplogroup A2 based on prior sequencing, I have a very unusual A2 haplotype (so far, the only one like it in the world). Haplogroup A2 is typically differentiated from the parent haplogroup A by changes at (at least) sites 146, 153, 16111, and 16362 in the control region and at sites 8027 and 12007 in the coding region. I, however, am missing the 16111T mutation.

As a result, at least one other company has had trouble determining whether I am A or A2. 23andMe, for example, bases its A2 classification on two sites, 8027 (rs1116904) and 16111 (i3001593). Since I’m missing the 16111 mutation, 23andMe classifies me as simply A rather than A2 (and although 23andMe tests the 12007 SNP (rs2853497), they don’t appear to use it in the A2 calculation).

Y-DNA Results

Pathway classified my paternal haplogroup as R1b1b2a1a1, a subclade of R1b which is defined by U106 (aka S21 or M405) (SNP rs16981293 at position 8856078).

R1b1b2a1a1 is believed to be roughly 3,000 to 4,000 years old, and originated in central/northern Europe. The haplogroup is shared by both Craig Venter and James Watson, the first individuals to have their complete genomes published. I further belong to a subclade called R1b1b2a1a1c, which is defined by S26 (at position 13025258). 23andMe does not test the S26 SNP, and it is not currently clear whether Pathway tests the SNP.

Included with mtDNA and Y-DNA results is a summary of the current understanding of the origin and history of the haplogroup, and a migration map which shows:

“The migration map shows approximately when your ancestor originated and where they migrated across the globe. You can move the pointer along the bottom of the map to see different timeframes, or click on other migration lines to see the patterns of different haplogroups.”

The results also include a navigable haplogroup tree and information about some famous people whose mtDNA or Y-DNA results are known.

Downloading SNPs

Although I am currently not able to download my SNP results, the Davies article at Bio-IT World noted that this will most likely be an option in the near future:

“For now, there is no easy mechanism to obtain the raw SNP/genotype results, as the other DTC companies provide (either via download or CD). But it is coming. ‘This is your information and you are certainly entitled to it,’ said Bornstein. Becker says the information will be made available as soon as Pathway is satisfied that the novel SNPs on its custom chip are validated.”

My Health Results

Unfortunately, I am not yet able to employ Pathway Genomic’s health test because I live in New York state. NY currently requires a physician’s involvement in DTC testing, which, in my opinion, is a paternalistic barrier between NY residents and their genetic sequence. Pathway noted that hopefully this problem will be fixed within the near future, at which time I will access and share my health results.