The Genetic Genealogist

ScienceNews reports that researchers led by Eske Willerslev at the University of Copenhagen are attempting to sequence the genome of legendary Native American “Sitting Bull” (see “Genome of a Chief”).

Earlier this year (2010), Eske Willersleve announced the successful sequencing of approximately 80% of the genome of “Inuk,” a man from Greenland who left behind a few small fragments of bone and four hairs frozen in permafrost when he died about 4,000 years ago (see “Long-Locked Genome of Ancient Man Sequenced”).  Using these ancient DNA sequencing techniques, Willersleve’s group is analyzing DNA from other samples.

One of these samples is a lock of hair from Sitting Bull.

Sitting Bull (c. 1831 – Dec. 15, 1890) was a Hunkpapa Lokota Sioux born in South Dakota.  Sitting Bull played an important role in the June 25, 1876 Battle of the Little Bighorn, and later toured as a performer in Buffalo Bill’s Wild West show.

It is not clear from the ScienceNow article, but the lock of hair being used for the analysis could be the same lock of hair that was repatriated to Ernie LaPointe, the great-grandson of Sitting Bull, in December 2007 (see “Assessment of a Lock of Hair and Leggings Attributed to Sitting Bull, a Hunkpapa Sioux, in the National Museum of Natural History, Smithsonian Institution”).  Ernie LaPointe is believed to be the closest lineal descendant of Sitting Bull, and one of his few remaining descendants (see “Smithsonian traces Sitting Bull’s descendants”).  The lock of hair was acquired from Sitting Bull’s body upon his death in 1890 by U.S. Army surgeon Dr. Horace M. Deeble, and when Deeble died in 1896 it was loaned to the National Museum of Natural History.

It’s unknown when the researchers plan to release their results.  The ScienceNews article mentions that one of the researchers, Cristina Valdiosera, revealed the plan to sequence Sitting Bull’s genome at an August 2010 scientific meeting:

“Valdiosera said that the researchers have the approval of Sitting Bull’s descendents to perform DNA tests on a sample of his hair, and that the team is trying to extract a full genome. If so, his would become the first ancient, non-frozen, Native American genome sequenced.”

Interestingly, it appears that working with Sitting Bull’s genome may be a life-long dream for Willersleve (see “Fossilized feces found in Oregon suggest earliest human presence in North America”):

“[Willersleve] said his own interest in the subject [of ancient American DNA] was sparked by a boyhood fascination with Sitting Bull and other American Indians.”

Sequencing Famous Genomes

As new techniques for sequencing ancient or low-quality DNA samples are developed, researchers will begin to analyze any famous or ancient genome they can get their hands on, which is already beginning to happen.  As a genealogist, I know very well the affiliation humans have for keeping mementos of the past.  There are probably hundreds of famous and ancient DNA samples waiting their turn for sequencing.

Off the top of my head, here are 5 people – either known or likely to have DNA kicking around – that I would nominate for analysis:

• Albert Einstein;
• Abraham Lincoln;
• Ötzi (I believe this one is already in the works);
• Juanita the Peruvian Ice Maiden (a 600-year-old mummy); and
• My great-grandmother Helen (hey, I can’t deny my genealogy side!).

Whose genome would you nominate for sequencing?

Ethical Issues

The ScienceNews article notes “the researchers have the approval of Sitting Bull’s descendents to perform DNA tests on a sample of his hair.”  Certainly they needed permission to obtain DNA from the hair clipping, but did they need permission to sequence that DNA? (setting aside for the moment the many ethical concerns regarding Native American remains).

For example, if I find a hair clipping in a book I purchased at an estate sale, do I have a duty to find the owner’s descendants and ask for permission before sending it away for sequencing?  What if the hair clipping is clearly labeled with the owner’s name and other identifying information?  Further, can I leave instructions for my descendants that they do not sequence or give permission to sequence my DNA?

I’m not a believer in genetic exceptionalism, so I look outside the realm of DNA for insight.  If that book I’d purchased at the estate sale was an old diary or journal, it most likely would not cross my mind to contact the author’s descendants before reading it.  And, interestingly, that diary or journal is much more likely to reveal personal information about the author than anything I could possibly discover in their genome.

What are your thoughts?  What permission might be required when sequencing ancient or famous DNA?

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.)

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.

Today at noon, the American Society of Human Genetics lifted an embargo on “Inferring Genetic Ancestry: Opportunities, Challenges, and Implications (pdf),” which will be published in the May 14^th issue of the American Journal of Human Genetics.

This paper is a follow-up to a 2008 paper called the “ASHG Ancestry Testing Statement and Recommendations” in which a committee from the ASHG addressed concerns about the claims made by genetic ancestry testing companies.  I wrote an article here on the blog at the time – The ASHG Ancestry Testing Statement and Recommendations – that highlighted a number of concerns I had about the statement and the recommendations.

When I wrote the November 13, 2008 blog post, I began by pointing out my personal positions, which have largely remained unchanged in the intervening 1.5 years:

• After years of experience in this field, I am a proponent of genetic genealogy testing, a scientific endeavor that has been utilized by more than 800,000 customers.

• I believe that education, not more government regulation, is the most efficient and appropriate answer to the issues raised by the authors of the paper.

• I believe that autosomal genetic genealogy testing is in its infancy and should only be used with the understanding that the results are only extremely rough estimates that are subject to change as the field develops.

The 2010 paper begins with a brief introduction and a table of most of the companies currently offering genetic ancestry tests.  The paper also discusses many of the issues associated with genetic ancestry tests, including: (i) the differing definitions of ancestry [of which there are many]; (ii) the tools for inferring ancestry; (iii) accuracy of those inferences; and (iv) ancestry and health, among several other things.

Overall, as discussed in great detail below, the authors have done an excellent job of addressing the concerns I raised in my review of their 2008 paper, which I felt was a much poorer review of the field (see below where I’ve compared my concerns from 2008 to the 2010 paper).

The 2010 paper ends with the following two recommendations:

• “Leadership of the human-genetics community, diverse in its interests and its own identities, should develop mechanisms for promoting thoughtful and rigorous use of genetic ancestry estimation in academic research.”

• “Interested scientific and scholarly societies should collaborate to convene a national roundtable discussion of DTC genetic ancestry testing.”

Interestingly, the second recommendation is similar to the one that I made after reviewing the ASHG’s 2008 paper when I stated that “I hope that the Task Force is actively conversing with people outside the committee, including commercial testing entities, researchers, and customers of genetic genealogy in order to obtain a well-rounded view of the field.”

Additionally, the 2010 paper specifically offers an “alternative approach” to federal regulation of genetic ancestry testing (something that I have often and repeatedly stated my disagreement with):

• “Recently, Lee and colleagues called for federal regulation of genetic ancestry testing.  At this juncture, we offer an alternate approach, one that might itself lead to federal oversight, if subsequently deemed appropriate, necessary, or practical.  We believe that effective decision making regarding genetic ancestry inference, in particular DTC genetic ancestry testing, will be best initiated through cooperative interaction among a variety of stakeholders, including suitable federal agencies.  Considering that such collective engagement has not yet occurred, it is premature to assume reticence or resistance on the part of any of the players or that federal regulation is the only recourse.”

I thought it might be an interesting exercise to determine whether the new paper addressed the concerns I raised after reading the 2008 paper.

General Concerns:

• The 2008 Paper – In 2008, I wrote that “[t]here are statements in the paper about psychological reactions to testing results, including the conclusion that ‘[t]he occurrence of or potential for emotional distress in people and groups following receipt of conflicting information about their ancestry has been well documented.’  Unfortunately, the statements are based on anecdotal stories or isolated examples rather than any systematic or scientific investigation of the reactions of individuals to the results of genetic genealogy testing.  I am unaware of any systematic objective study that looks at the reactions of individual to genetic genealogy testing results (outside of the paternity test or health testing arenas).  Indeed, a prior policy paper from the ASHG cites only a BBC documentary that examined the ancestry of three individuals of African descent and a newspaper article to support their conclusion that “[t]est-takers may…suffer emotional distress if test results are unexpected or undesired.”  I would suggest that the Task Force, rather than assume that this “emotional distress” response to genetic genealogy test results has been well documented, conduct an objective study specifically tailored to analyze genetic genealogy testing. The difference between the results of genetic genealogy testing and the results of health or medical testing is so vast that drawing comparisons between the two is extremely problematic and potentially inaccurate.

• • The 2010 Paper – The new paper states that “Knowledge about genetic ancestry, particularly if undesirable and unexpected, can lead to the reshaping of group, familial, or personal identity (cites omitted)…The occurrence of, or potential for, emotional distress in people, families and groups after receipt of conflicting information about their identity through DTC ancestry testing has also been discussed [cites omitted]. Nonetheless, some research focused on consumers of ancestry testing has revealed that although ancestry tests might promote genetic thinking about ancestry and ‘‘race,’’ test takers also were able to construct meaningful narratives of their identity. [citing to Alondra Nelson’s article; see Article Review: “Bio Science: Genetic Genealogy Testing and the Pursuit of African Ancestry”].  Clearly, additional empirical research will need to adequately explore the relationship between genetic ancestry testing and the identities and overall psychological well-being of test takers, their families, and their communities.”

• • Thus, the 2010 statement clearly weakened the stance of negative perceptions from “well-documented” to “has been discussed,” and cites Dr. Nelson’s very interesting research, which suggests that test takers interpret results to meld with their preconceived identity.  The section ends by suggesting that more research is needed, which I suggested in my 2008 review.

• The 2008 Paper – In 2008, I wrote that “[t]he paper muddles the distinction between Y-DNA/mtDNA testing and autosomal testing, even though the differences are huge.  The results of Y-DNA and mtDNA tests are STR numbers, SNP designations, or differences from the CRS which are then used to estimate a haplogroup or compare with another’s results.  Given the extensive data regarding haplogroup designation, the estimates are highly accurate.  Additionally, a haplogroup designation implies only a very broad geographical origin many thousands of years ago; it is not an estimation of genetic ancestry, as the authors of the policy paper imply.  Haplogroup designations have existed for more than 20 years and continue to be used by population geneticists and anthropologists.  The results of autosomal testing, however, are estimations of genetic ancestry.  These autosomal tests look at anywhere from 13 to 500,000 locations – out of billions – on the human genome and return percentages of ancestry based on those markers.  Autosomal testing can be confusing to test-takers because customer often assumes that the percentages are final and represent an accurate picture of their entire genome.”

• • The 2010 Paper – The 2010 statement more clearly breaks up the analysis into the very different fields of “mtDNA and Y Chromosome Markers” and “Autosomal Variants” in one section, and “Lineage Identification with Uniparental Markers” and “Admixture Estimation” in another.

• The 2008 Paper – In 2008, I wrote that “[t]he authors mix the issues associated with the everyday genetic genealogy test-taker with the issues faced by very specific groups of test-takers.  For example, Native American groups are concerned about the effects that genetic genealogy will have on group identity and membership.  These same concerns have also been raised by lineage societies such as the SAR and the Mayflower Society.  Any regulations that a group believes it needs should be at the level of the group, not at the level of the testing! Groups that have these concerns should themselves decide whether and how to use genetic genealogy results for membership and group identity (such as the DAR and Mayflower Society are doing); regulating genetic genealogy at the testing level is not the most efficient or appropriate way for these groups resolve the ethical and social concerns.”

• • The 2010 Paper – The 2010 statement has a section on page 10 that addresses this issue.  It states that “[r]eports of the use (or intended use) of ancestry test results to make claims for benefits through affirmative action or for rights perceived to be associated with their new-found Native American status have increased unease over the loss or gain of certain rights or entitlements,” but reasonably notes that “It remains to be seen what tangible effects (if any) genetic ancestry inference will have on these pre-existing entitlement issues.”  Here, again, the ASHG has addressed my concerns.

• The 2008 Paper – In 2008, I wrote that “[t]here is mixing of the controversial phrase “direct-to-consumer” with genetic genealogy.  Of course it’s direct-to-consumer, who else would the results go to?  Surely the authors of the paper aren’t suggesting that genetic genealogy tests should be ordered and reviewed by a doctor or genetic counselor.  That would be a ridiculous restriction.”

• • The 2010 Paper – The 2010 statement still uses the term DTC, but I think in the last 1.5 years the use of the term in general has been to indicate that the testing is done without the use of a doctor or counselor rather than to suggest that a doctor or counselor should be involved.

• The 2008 Paper – In 2008, I wrote that “[a]lthough I am unaware of the composition of the ASHG Task Force, I hope that it is made up of a diverse group. Additionally, I hope that the Task Force is actively conversing with people outside the committee, including commercial testing entities, researchers, and customers of genetic genealogy in order to obtain a well-rounded view of the field.”

• • The 2010 Paper – The 2010 statement, very much in line with my 2008 recommendation, concludes with the recommendation that there be a “face-to-face conversation among ancestry-testing companies and promoters, consumers, community leaders, advocacy and interest groups, geneticists, social and behavioral scientists, humanists, healthcare providers, legal professionals, federal agencies, media, and other key stakeholders should be to identify major issues of concern and brainstorm practical solutions.”

Thus, with this paper the ASHG appears to have addressed almost every one of the concerns and misconceptions I raised in my review of the 2008 statement and recommendation.  Actually, it’s almost uncanny.  I applaud the committee for their work and thank them for addressing these issues.  Hopefully, when the ASHG’s proposed “national roundtable discussion of DTC genetic ancestry testing” is convened, I will be able to attend.

Daniel Vorhaus of the Genomics Law Report is also a member of the steering committee of the GET (“Genomes, Environments, Traits) Conference 2010. This unique conference, to be held on Tuesday, April 27, 2010 will gather together some of the biggest names in personal genomics, as well as most of the limited number of the people who have released their entire genomes to the public. Tickets for the conference go on sale today here.

As part of the GET Conference 2010, the new BioWeatherMap initiative will officially launch. According to the project’s website, BioWeatherMap is “a global, grassroots, distributed environmental sensing effort aimed at answering some very basic questions about the geographic and temporal distribution patterns of microbial life. Utilizing the power of high-throughput, low cost DNA sequencing and harnessing the drive of an enlightened public we propose a new collaborative research approach aimed at generating a steady stream of environmental samples from many geographic locations to produce high quality data for ongoing discovery and surveillance.”

Unfortunately I will be unable to attend the GET Conference 2010, although I’m sure I and anyone else interested in the Conference will all be able to participate in at least a limited manner through social media.

The Press Release

Personal Genome Pioneers to Convene at the Inaugural Genomes Environments Traits (GET) Conference: Luminaries at landmark gathering to shed light on diverse impact large-scale personal genome sequencing will have on everyday life

BOSTON, Mass. (February 18, 2010) — Worldwide fewer than 20 individuals have had their genomes sequenced and made publicly available, and on Tuesday, April 27, for the first time, nearly all of them will appear together, along with a select group of business leaders and scientific visionaries, to share their experiences and to provide a look ahead at how personal genomics will rapidly and broadly impact society. This historic gathering will take place at the inaugural Genomes Environments Traits (GET) Conference as part of a day-long thought leadership forum, exploring the myriad ways in which the integration of personalized genomic, environmental and trait information will shape the ways in which we access and interact with our genetic information.

“The GET Conference 2010 marks the last opportunity in history to gather a majority of individuals in the world with public personal genome sequences in a single venue,” says George Church, founder and principal investigator of the Personal Genome Project and professor of genetics at Harvard Medical School. “With rapid advances in technology, the number of individuals with personal genome sequences is expected to rise dramatically, from dozens today to thousands by 2011 and a million or more individuals within the next few years.”

The morning portion of GET Conference 2010 will feature wide-ranging discussions during which personal genome pioneers and globally recognized leaders of genomic science and industry, including Misha Angrist, George Church, Jay Flatley, Henry Louis Gates, Jr., Rosalynn Gill, Seong-Jin Kim, Greg Lucier, James Lupski, Stephen Quake, Dan Stoicescu and James Watson, will share their experiences and discuss the future of personal genomics. Award-winning science journalists Carl Zimmer and Robert Krulwich will moderate the discussions.

These experts will re-convene in the afternoon for a series of breakout sessions with other thought leaders and conference participants in a series of intimate discussions focused on the role personal genomes play in understanding ancestry, family life, nutrition, and disease risk, as well as the marketplace for products and services that utilize the analysis of genomic and environmental information, including new drug therapies, consumer products and law enforcement applications.

The afternoon program will additionally showcase:

• Four “prototypes of the future” sessions highlighting the next generation of personalized genomic products, services and activities and moderated by the executive editor of WIRED and author, Thomas Goetz.

• The public debut of the BioWeatherMap initiative, a collaboration between scientists and the public using next-generation sequencing platforms to address the fundamental question: “How diverse is the microbial life around us and how can we use that information to our advantage?”

The GET Conference 2010 will take place on Tuesday, April 27, 2010 from 8:00 a.m. – 8:00 p.m. at the Microsoft New England Research and Development Center in Cambridge, Mass. The event will be limited to 200 registrants. To register for the GET Conference 2010, visit http://www.getconference.eventbrite.com/.

About the GET Conference 2010

The first annual GET Conference will gather 200 scientific, industry and thought leaders in the fields of personal genomics, personalized medicine, microbiomics and systems biology, as well as prominent hedge fund managers, VCs, private investors, and philanthropists, in an intimate venue to consider the present and future of personal genomics.

All proceeds from the GET Conference will benefit PersonalGenomes.org, a 501(c)(3) charitable organization which supports the Personal Genome Project and whose mission is to serve as a global ambassador for emerging technologies and knowledge that will positively impact the health and well-being of humankind. For more information, visit www.getconference.org, or e-mail info@getconference.org.

Conference sponsors include: Alan & Priscilla Oppenheimer Foundation; Knome; Life Technologies; Microsoft; OHO Interactive; Procter & Gamble; Robinson, Bradshaw, & Hinson; Schwartz Communications; and Third Rock Ventures. Limited sponsorship opportunities are still available. For more information email: info@getconference.org.

About the Personal Genome Project

The Personal Genome Project is an open-ended research study that aims to improve the understanding of genetic and environmental contributions to human traits. The project is currently enrolling members of the public who are willing to share their genome sequence and other personal information with the scientific community and the general public. For more information, visit http://www.personalgenomes.org/.

I once told someone that in addition to learning about their ancient origins (such as Y-DNA and mtDNA haplogroups), many genetic genealogists would ideally like to match every portion of their DNA with the contributing ancestor.  Although this might seem to be beyond the reach of current genetic ancestry testing, it has actually already begun.  The family compare function of 23andMe, for example, is already being used by genetic genealogists for just this purpose; people who have matching DNA segments can compare ancestry and attempt to identify the ancestor who might have contributed the DNA.

For obvious reasons, medical geneticists have for many years been using genealogy to trace founder mutations in populations.  For example, in 2008 scientists traced a colon cancer gene in the United States to a Mr. and Mrs. George Fry who arrived in the New World around 1630 (see A Single Colon Cancer Gene Traced to 1630).

Tracing A Heart Disease Gene in South Africa

Now, scientists in South Africa recently announced that they had traced a gene responsible for a hereditary heart disease called familial heart block (PFHB) to a Portuguese immigrant who arrived in South Africa in 1696.

From the article:

“The rogue gene was found in three branches of an Afrikaans familial group that can trace its ancestry back to one Portuguese individual who landed on the shores of the Cape at the end of the 17th century.

Prof Andries Brink, former dean of Stellenbosch University’s faculty of Health Services, first described the disease in 1977 and published a paper at the time in the South African Medical Journal. The paper, titled Progressive familial heart block – two types, was co-authored by genealogy specialist Marie Torrington.

It was Torrington who discovered that the disease was brought into South Africa by the Portuguese immigrant who arrived in South Africa in 1696. He subsequently married a woman of Dutch descent, and genetics has carried PFHB down all the generations since then. No matter where in the country they live, every South African suffering from PFHB today is descended from that couple.”

The Journal of Clinical Investigation article is here.

As part of her doctoral research, Sudeepa Abeysinghe is asking people who have purchased genomic tests to complete the “User Experiences of Direct-to-Consumer Genomic Testing Survey”.  According to Sudeepa, the survey focuses on the consumer experience and is completely independent of any testing company.

Although I’m late on reporting this (it was already covered by GenomeWeb, for example), I thought I would mention it in case anyone has missed the previous coverage and might be interested in completing the survey.

This is an opportunity for genetic genealogists to share their experiences and voice their thoughts regarding DTC genomic testing.

An article in the United Arab Emirate newspaper The National (wikipedia) does a terrific job of highlighting recent research from Family Tree DNA.  The story – “DNA could illuminate Islam’s lineage” – discusses research that has attempted to elucidate the Y-DNA signature of Mohammed.  Although Mohammed did not have a son, he had a daughter who married her paternal second cousin, thus passing to Mohammed’s grandchildren the same Y-DNA.  From the article:

“For almost 1,600 years, the title Sharif, Sayyed, or Habib has been bestowed on Muslims who have been able to trace their roots back to the Prophet Mohammed through intricate family trees, oral histories and genealogical records. But now an American DNA lab says it may have identified the DNA signature of descendants of the Prophet Mohammed, and perhaps the prospect of a direct, more accurate means of confirming or identifying such a connection.”

The caveat, as the story briefly mentions by the phrase “if their oral tradition is accurate”, is that no one has an authenticated DNA sample directly from Mohammed.  If there were, this type of research would not be needed.  Instead, the conclusion that it might be Mohammed’s Y-DNA is based on testing individuals who are likely to be descended from Mohammed and looking for a common Y-DNA signature.  Until a DNA sample from Mohammed is obtained (likely an impossibility), the conclusion will not be 100% proven, which means that any information about this conclusion should also contain info about this caveat.  Of course, as all genealogists know, almost none of our conclusions about ancestry/descendancy are 100% proven, especially when they are based at least in part on oral and paper records.

Sharifs DNA Project at FTDNA

There is a public Sharifs DNA Project at Family Tree DNA, which contains the following information:

“Sharif’s are people who claim to be descendant from the Prophet Muhammad, Peace on him, through the two sons of his daughter Fatima Ezzahra, which are Hassan and Hussein. The descendants of Hassan and Hussein sons of Ali Ibn Abi Taleb spread all over the world and particularly in the muslim world from Indonesia to Moroco. There are actually hundreds of thousand of people who are claiming to be be Sharifs. Some of them have a lot of genealogy documents heritated from fathers to sons and which contain many data about the genealogy trees.”

Perhaps the deduced Y-DNA signature is there?

Twitter

I first announced this story early this morning via twitter.  If you are a twitter user and would like to follow me, just click below:

Image by Aaron Logan

Roughly 6 million years ago, the Hominini subtribe of the Hominidae family tree (the so-called “great apes”) diverged into two known branches, with one branch (genus Pan ) resulting in modern-day Chimpanzees and Bonobos, and the other branch (genus Homo) resulting in modern-day humans.

Since there has only been 6 million years of divergent evolution, Chimpanzees/Bonobos and Humans share a great deal of DNA sequence in common (although estimates vary widely and typically depend on what, exactly, is being considered in the comparison).

The Close Cousins DNA Project

On May 31, 2008, the Close Cousins DNA Project was launched by Bill Davenport as a result of a discussion on the Genealogy-DNA mailing list regarding the relatedness of human and chimpanzee Y-DNA.  From the launching post:

Three days ago, John Marsh sprung on us the idea of testing a chimpanzee on FTDNA’s standard 67 Y-DNA STR markers. To quote John: “Chimpanzee and Bonobo are sufficiently different to each other, and to humans, to make differences between their Y-DNA markers potentially interesting, and give insights into how mutations of Y STRs have wandered along over very long time periods. The common ancestor of humans and Chimps is about 100 times longer than the common ancestor of all human male lines”  Today, I am announcing the formation of the Chimpanzee Y-DNA Project. In FTDNA’s database it will be a Y-Haplogroup project and the official name is Close_Cousins. The original goal is for fun and curiosity since we don’t really know what we’ll get. But hopefully we make some interesting discoveries that may prove useful and encourage further research.

Goals of the Close Cousins Project

One of the goals of the Project is to obtain a DNA sample from a chimpanzee and a bonobo (preferably a cheek swab) and have it analyzed at 67 STR markers by Family Tree DNA.  Although the project has graciously received funds from a number of donors (see here for a list of these scientifically curious and kind donors) that will enable the purchase of a regular 67-marker test from FTDNA, there will almost certainly be extra analysis required due to 6 million years of sequence divergence.  However, Bennett Greenspan of FTDNA has kindly offered to cover the costs associated with extra processing.

Why compare the human Y-STR markers with the chimpanzee markers?  Aside from merely satisfying intellectual curiosity, this project could reveal interesting information about the mutation rates of some markers, among other information.

A Request for Help

Last December, I became a co-administrator of the Close Cousins Project with Bill Davenport.  As such, I am requesting your help in advancing this project.  Our biggest current hurdle is identifying a source of chimpanzee and bonobo Y-DNA.  Do you have any insightful ideas to share about how to obtain the necessary DNA?  Do you have an acquaintance who might have [legal] access to chimpanzees and/or bonobos?  Know someone who owns a chimpanzee and/or bonobo? We would appreciate any helpful suggestions or connections in our pursuit of this project.

A Postscript

Lastly, as a law student I am cognizant of the fact that collection of DNA from a non-human primate – even using a painless mouth swab – might trigger some state and/or federal regulations.  I am working to ensure that the project satisfies these regulations when collecting DNA from primates.

Image via CrunchBase

DAVIDE at the European Genetics and Anthropology Blog recently posted two interviews (here and here) with customers of 23andMe’s large-scale genome scanning service, one from Finland and one from the U.S.

It’s very interesting to see the responses of these anonymous individuals, particularly since they are from different countries.

For example, both were asked why they decided to purchase the 23andMe test – “Was it to test your ancestry or genetic health risk factors?”  Interestingly, for both individuals ancestry was the motivating factor behind testing.  More support for my conclusion that these companies should strongly promote the ancestral aspects of their products.

Other Questions

Here are a few examples of other questions in the interviews:

Q: How would you rate the accuracy of the scan against what you know about your origins?

Q: Has the information about your ancestry changed how you now identify ethnically or look at certain cultures or world regions? For example, do you now show more interest in Asia knowing that you have some East Asian admixture?

Q: Were you in any way disappointed with the results? For example, were you let down by where you ended up on the genetic maps or who your closest individual matches were?

Q: Looking back, was the experience worth the $399? Will you recommend the test to your family and friends?

If you are thinking about testing at a genome scanning company, be sure to read these interviews to get a feel for the process.

HT: Daniel MacArthur at Genetic Future.