The Genetic Genealogist

In October 2008, I reviewed an article by Dr. Alondra Nelson in the journal Social Studies of Science entitled “Bio Science: Genetic Genealogy Testing and the Pursuit of African Ancestry” (Social Studies of Science 2008 38: 759-783).  The article was about the complex interpretation of the results of genetic genealogy testing by African-Americans and black British.  Dr. Nelson is Associate Professor of Sociology at Columbia University in NY.

On Friday, an article by Dr. Nelson appeared in The Chronicle of Higher Education entitled “Henry Louis Gates’s Extended Family,” which is an introduction and review of the current PBS documentary miniseries Faces of America. Regarding the genetic testing aspect of the show, Nelson writes:

If the findings of conventional genealogical research produce fireworks, the results of the DNA analysis generate shock and awe. “Know Thyself,” the final episode, which shares its title with the slogan of Knome Inc., focuses mostly on genetic genealogy. Whereas prior shows relied heavily on analysis of mitochondrial DNA (mtDNA) and Y-chromosome (Y-DNA), yielding results that included at most about 2 percent of one’s complete genetic inheritance, in Faces techniques are used that probe deeper into more of the genome.

The technical aspects of genetic ancestry tracing are explained, but without sufficient social context, much the way a manual can tell you how to operate a car without explaining automobiles’ role in modern industry, the development of suburbia, or the emergence of youth culture. We can’t hold a documentary for a general audience responsible for not presenting a complex metanarrative on the philosophy of genetic science. But we can expect some acknowledgment and interpretation of technology’s limits.

It is likely that some genetic genealogists will instantly disagree with or discredit Nelson after reading this article, since it might appear that she is being critical of genetic genealogy, but I would disagree.  In my opinion, however, it is important to be aware of Nelson’s concerns, since they are concerns shared by many people across the globe.  For better or for worse, Faces of America will be many individual’s first introduction to genetic genealogy, and without seeing the whole series yet, I hope that Gates does a fair job of introducing this wonderful technology without glossing over its limitations, particularly as they might apply to minority or marginalized populations.

That being said, I also believe that the individual shares the responsibility for understanding this technology before deciding to undergo testing.  We are all responsible, in part, for our own education.

Rather than discrediting genetic genealogy, I believe that Nelson embraces the ability of genetic testing to help some people – and ultimately society – understand our present and our past, as well as how we are all so closely related, either through our genetics or through our shared history.  Indeed, the end of the article ends with the note that Nelson “is at work on a book about genetic ancestry tracing and African diaspora culture,” which I look forward to reading.

What are your thoughts after reading Dr. Nelson’s article?

Faces of America continues every Wednesday evening from 8 – 9 p.m. ET on PBS stations through March 3rd.

• DNA Test Index has a great index of DNA testing providers, including genetic genealogy testing companies.  Via @genomicslawyer – an atypically complete list of genetic test providers: http://bit.ly/2f8FLW.

• ISOGG, the International Society of Genetic Genealogy, has a new information page at “I’ve Tested at 23andMe, Now What?“  The site includes a variety of tools to help you further explore your ancestry, including EURO-DNA-CALC and Promethease, among others.

• Family Tree DNA has a new Holiday Sale, as summarized at the U4 Haplogroup website.  The FTDNA ordering page also has the holiday prices.

• Linda Avey, co-founder of 23andMe, has started a new blog entitled The Life & Times of Lilly Mendel.  I’m looking forward to some interesting reading as Linda establishes the Brainstorm Research Foundation dedicated to the study of Alzheimer’s disease.

• The Genomics Law Report continues the fascinating What ELSI is New? series, including a contribution from yours truly.

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.

In the past week there have been so many articles and posts about either genetic genealogy or DTC genetics that I’m writing them up as a summary post rather than individually.

The New York Times Tackles DTC Genetic Testing

An article in yesterday’s New York Times by Jane E. Brody – “Buyer Beware of Home DNA Tests” – argues that DTC genetic testing is fraught with danger (the article and some of Brody’s arguments are summarized by Grace Ibay of Genetics & Health: “Seven Reasons Why Home DNA Tests Are Hype”).  The author even lumps in genetic genealogy (which has been around for over 9 years now, hardly a “new industry” that has sprung up “to cash in” on new science):

“As a source of entertainment at so-called spit parties or an effort to trace genetic ancestry, the tests might be seen as relatively harmless (unless someone is appalled to discover who their ancestors might be).  But for the many people who are bypassing the medical profession to determine, they believe, how likely they are to develop a life-threatening disorder, experts say direct-to-consumer genetic testing is fraught with potential dangers.”

Oh no, people might be “appalled” to discover their ancestors!  I can assure you that people were “appalled to discover who their ancestors might be” long before DNA testing!!  If the results of genetic genealogy testing upsets people, the government better outlaw census records, historical societies, and grandma’s stories after Thanksgiving dinner because the information you’ll receive there will surely be much more ‘appalling.’

Jen McCabe has a terrific thought-provoking rebuttal to the NYT article at ‘Jen’s Posterous’ – “Paternalism and “Patient Beware” Messages Hit DTC Genomic Testing.”  McCabe does a great job of deconstructing the arguments and countering them with her own.  I’ll admit that I’m terribly biased here, but I think that McCabe raises some excellent points.

I wouldn’t be surprised to see more response to this article, including perhaps at Genetic Future or Genomics Law Report.

Dr. Michael Hammer, the Ancestor Hunter

Miller-McCune has a great article – “The Ancestor Hunter” – about the University of Arizona’s Michael Hammer, who is a major contributor to the field of genetic genealogy.  Many readers will know that Dr. Hammer is also FTDNA’s Chief Scientist.  From the FTDNA about page:

“A Biotechnology Research Scientist at the University of Arizona with appointments in the Department of Anthropology and the Department of Ecology and Evolutionary Biology, as well as Director of the Genomic Analysis and Technology Core facility, Dr. Hammer received his PhD in Genetics from the University of California at Berkeley and was a post-doctoral fellow at Princeton and Harvard Universities. He co-authored the first paper showing that present-day Cohanim are descended from a single male ancestor.”

The article discusses Dr. Hammer’s work in the field, including Native American studies, Cohanim relatedness, and co-founding the DNA Shoah Project, for example.

Questioning a Journalist’s Humanity

A few weeks ago I corresponded with journalist Peter Aldhous of NewScientist magazine about his mtDNA results from deCode Genetics.  Without any other information, he wondered if I could identify the probable haplogroup of two mtDNA samples.  One was easily identifiable, while the other was such a garble that I was thrown for a loop.  So, just to be sure, I wrote back to Peter and asked him a now-infamous question:

“This is a strange question, but are you sure this is Homo sapiens?”

Peter writes in his article:

“It’s not every day that an expert queries whether your DNA is human, so when I received this comment by email earlier this month I was somewhat bemused.

“I am not in fact the result of a coupling between human and alien, nor the product of some twisted genetic experiment. Instead, Blaine Bettinger, who blogs as The Genetic Genealogist, had been baffled by a DNA profile generated in error by deCODEme, a leading commercial “personal genomics” service provided by Decode Genetics in Reykjavik, Iceland. The false profile seems to be the fault of a software bug.”

The article was mentioned by GenomeWeb – “You Are Human, Right?” – and there are two extremely good blog posts about the article and the situation by Daniel MacArthur at Genetic Future – “There’s many a slip ‘twixt spit and SNP: errors in personal genomics data” and Dan Vorhaus at Genomics Law Report – “Leveraging the Crowd to Understand Your Genome.”

So what is the take-home message?  Of course it is not that DTC genetic testing is dangerous or requires government regulation; rather, it is that both DTC companies and consumers must be diligent.  As MacArthur writes:

“But the most important piece of advice for personal genomics customers is to engage with your data.  Aldhous only detected these anomalies because he was exploring his own genetic data in multiple ways, cross-checking it against both other data and his own (informed) expectations, and was persistent enough to follow up on the strange results he found.

“That’s a good example for other personal genomics customers to follow: rather than being a passive recipient of genetic forecasts, dig into your data and see if it makes sense, and keep asking questions until it does. In addition to making it more likely that you’ll pick up any errors in your results, you’ll also develop a much deeper understanding both of the nature of genetics and of your own genome.”

And Vorhaus posits that traditional sources of genetic interpretation – i.e. physicians – might be supplemented by other sources, including genome sharing:

“From unraveling bioinformatics errors, as Aldhous did, to adjusting medications, to uncovering unknown genetic variants, the upside of utilizing an open-access approach to personalized genomic interpretation is the ability to allow an untold number of eyes to comb over your data in search of something important (or perhaps just interesting). It seems highly improbable that any combination of DTC genomics companies and open-source genomics resources will ever completely supplant a one-on-one consultation with a trained medical professional, particularly where clinical genetic guidance is required. And concerns over privacy and misuse of data may inhibit many from sharing their own genomic data, at least at present. But there appears to be a significant role for open-source genomics resources to play in the continuing expansion and democratization of personal genomic inquiry.”

I encourage anyone who is interested in DTC genetic testing or just genetic genealogy to read through some of these articles to get a feeling for some of the issues that are currently being discussed regarding this field.

Another great article from the Genomics Law Report (if you aren’t already reading this new blog, you should be) – “Is the ACCP’s Call for Greater Governmental Regulation of DTC Genetics Premature?”

Barbara Ameer and Norberto Krivoy of the American College of Clinical Pharmacology (ACCP) have an article (pdf) in The Journal of Clinical Pharmacology that promotes regulation of DTC genetic tests (which could conceivably include genetic genealogy tests).  The Genomics Law Report analyzes the paper’s arguments and concludes with the following:

“Without convincing evidence of the harms of DTC genetic testing, it remains difficult to fully justify more rigorous governmental regulation, or to anticipate its content, structure or ultimate effect, which perhaps explains why such regulation continues to remain just over the horizon.”

If you’re interested in this area, click over to the Genomics Law Report and read this article (as well as the original ACCP article).

Today, the Sorenson Molecular Genealogy Foundation (SMGF) reported that they are adopting a standardized Y-STR reporting system proposed by the National Institute of Standards and Technology (NIST) of the U.S. Dept. of Commerce and supported by the International Society of Genetic Genealogy (ISOGG).

The standardized system was first published in the Fall 2008 issue (pdf) of the Journal of Genetic Genealogy (JoGG).

First, let me add a note of caution – this change ONLY represents a change in how results are REPORTED.  Even though companies report results differently, this does not mean that the actual DNA testing results are wrong or different!  This shift is NOT to correct errors in testing results; it is only to standardize reporting.

From the Press Release:

SALT LAKE CITY (Aug. 17, 2009)-The Sorenson Molecular Genealogy Foundation (SMGF) today announced it has implemented a recently developed industry-standard format for expressing Y-chromosome DNA profiles in genetic genealogy. The new system, or nomenclature, for Y-STR genetic markers will reduce confusion for genetic genealogy consumers, eliminate conversion errors, make personal DNA profiles easily portable and lead to more genetic matches when searching among different ancestry databases once the industry-wide standard is adopted. Y-DNA is an unrivaled tool for tracing paternal ancestry. Only males have the Y-chromosome, which is passed down virtually unchanged from father to son.

SMGF, a non-profit scientific organization with the world’s largest collection of correlated genetic and genealogical information, is the first to adopt the new system proposed by the National Institute of Standards and Technology (NIST) of the U.S. Dept. of Commerce and promoted by the International Society of Genetic Genealogy (ISOGG). Genetic genealogy is the application of genetics to traditional genealogy and is a component of ancestry research experiencing strong growth through personal DNA testing and online ancestry databases.

“We strongly believe this industry-wide standard benefits everyone,” said Natalie Myres, director of research and development for SMGF. “DNA profiles will become more useful to consumers because they will not have to use a conversion process to search different genetic genealogy databases. For DNA laboratories and providers, this common nomenclature leads to greater reporting accuracy and saves time explaining to customers why their results appear different from those of another provider.”

Until now, genetic genealogy companies and laboratories reported Y-STR genetic markers in DNA profiles to customers in various formats developed for forensic DNA reporting. “As DNA testing for genetic genealogy purposes has become common and more people put their DNA profiles into online ancestry databases, the need for a universal format became apparent,” said Katherine Borges, ISOGG director.

“This is a big benefit to consumers,” said Borges. “They will definitely find more matches because of this new standard. Currently, consumers are often unaware they have to convert their results for use on different databases or are intimidated enough by the process that they don’t check a variety of databases. Also, some errors find their way into conversion tools. All these problems reduce chances of finding matches.” Borges estimates close to one million DNA tests for genetic genealogy purposes have been purchased to date.

The three largest U.S. providers of genetic genealogy DNA testing have committed to adopting the new Y-STR reporting standard and Borges expects the others to follow suit. NIST has not recommended a uniform reporting standard for mtDNA, the genetic material passed down from mother to child.

About Sorenson Molecular Genealogy Foundation
The Sorenson Molecular Genealogy Foundation (SMGF; www.smgf.org) is a non-profit research organization that has created the world’s largest repository of correlated genetic and genealogical information. The SMGF database currently contains information about more than seven million ancestors through linked DNA samples and pedigree charts from more than 170 countries, or approximately 90 percent of the nations of the world. The foundation’s purpose is to foster a greater sense of identity, connection and belonging among all people by showing how closely we are connected as members of a single human family. For more information about the foundation’s free, publicly available database, visit www.smgf.org.

Ancestry Magazine has a new article by Megan Smolenyak about the use of Y-DNA testing to examine the origins of the Haley maternal line.

Chris Haley, nephew of Roots author Alex Haley, underwent Y-DNA testing.  After receiving the results which showed European origin (Haplogroup R1b), the results sat in the database for 18 months before a match was found.  Many of us have similar experience; our results are recorded and available but are waiting for the day we find a match.

Haley was lucky, however, and he was soon in contact with the family.  From the article:

Thomas [Baff, the individual that Haley tried to contact] turned out to be June Baff Black, Thomas’s daughter, who responded (she was thrilled!). June’s parents had researched the family back in the 1980s; June’s own involvement had started while watching an episode of Who Do You Think You Are? She’d been fascinated by Colin Jackson’s DNA test, ordered a test for her father, her Y-DNA stand-in, and mailed if off only a few weeks before hearing back from Chris.

This is just one example of the successes that the popular WDYTYA series has prompted.  I’ve heard a number of other stories about people gaining an appreciation for and interest in genealogy after watching the show.

The Ancestry Magazine article has much more about Chris Haley’s “reunion” with this family, and RootsTelevision has a video: “Haley-Baff Genetic Family Reunion.”

In March I announced the unofficial launch of Pathway Genomics, a new company offering genome SNP tests (Note: I am a consultant for Pathway Genomics).  Today the company officially launched, and their press release is below.  There is also an article at Bio-IT World (“Pathway Genomics Joins the Direct-to-Consumer Genomics Parade”).

Press Release:

Pathway Genomics Brings Together Renowned Team of Entrepreneurs, Scientists, Physicians, and a Government Certified Lab to Offer Personal Genetics Services

San Diego, Calif., July 15, 2009—Pathway Genomics, a privately held, venture‐backed company, today announced its launch, including the company’s web site, www.pathway.com. Pathway Genomics offers affordable genetic tests for under $250, enabling consumers to confidentially learn about their risk for various diseases, adverse drug responses, carrier status, and ancestral history. Leveraging customized and highly innovative DNA genotyping technologies, Pathway Genomics generates the most extensive analysis of an individual’s risk for disease and can trace the path of a person’s maternal and paternal ancestry back more than 150,000 years.

Pathway Genomics is located in San Diego, California and is the only U.S. based direct‐to‐consumer DNA genotyping company with California and CLIA (Clinical Laboratory Improvement Amendments) certification for its wholly owned and operated onsite laboratory. By obtaining both state and federal approvals, Pathway Genomics’ quality standards ensure that genetic information delivered directly to the customer is highly confidential, accurate, and reliable.

“In addition to a strong team of scientists who have made cutting edge discoveries in genetic diseases such as Alzheimer’s disease and diabetes, we’ve brought together a seasoned group of entrepreneurs and marketing experts to launch Pathway Genomics,” said Jim Plante, Founder and Chief Executive Officer of Pathway Genomics.

Pathway Genomics was founded by Mr. Plante, who brings over a decade of experience in technology and preventative health having founded four venture capital‐backed technology companies and launching more than 12 new product lines and services in the consumer products, automotive, wireless, and risk‐management service industries.

Pathway Genomics’ scientific team, consisting of top experts in molecular genetics, biostatistics, and genetic counselors is headed by David Becker, Ph.D., Chief Scientific Officer. Dr. Becker is most notably recognized for his contribution to Alzheimer’s research. While working at Torrey Pines Therapeutics, Dr. Becker’s team, in conjunction with Rudolph Tanzi, Ph.D., of Massachusetts General Hospital and Harvard Medical School discovered and validated genes that contribute to the pathogenesis of Alzheimer’s disease. This discovery was recently acknowledged by Time magazine as the #5 medical breakthrough in 2008.

“Evaluating an individual’s genetic profile is important, but it only reveals part of a person’s health and wellness. The overall picture should also include information about a person’s family history and lifestyle,” said Dr. Becker. “For this reason, we want our consumers to take control of their health by identifying areas in their life that they could change to reduce their risk for developing diseases.” The Founders Fund, Edelson Technology Partners, and Western Technology

Investment provided principle funding for Pathway Genomics. The Founders Fund has invested in a number of high‐tech companies including Facebook, SpaceX, and Quantcast, Edelson Technology Partners has invested in well‐known multinational corporations including Websense and Celgene, and Western Technology Investment has recently invested in PEAK Surgical and EnteroMedics.

Additional information about Pathway Genomics, including a list of diseases, drug responses, and ancestral haplogroups tested using Pathway Genomics’ health and ancestry kits, plus sample reports and step‐by‐step ordering instructions can be found at www.Pathway.com. For the first 500 people to log on to the site, order a kit, and enter the code MYPATH a 15% discount will be applied to the total order.

About Pathway Genomics

Located in San Diego, California, Pathway Genomics is a privately‐held, venture‐backed company that offers affordable, personal DNA genotyping tests for less than $250. As the only U.S. based direct‐to consumer genetic testing company to receive both California and federal Clinical Laboratory Improvement Amendments) CLIA for its wholly owned and operated onsite laboratory, consumers can access health and ancestry tests to learn about their disease risks, adverse drug responses, disease carrier status, or ancestral history. More information about Pathway Genomics can be obtained by visiting www.Pathway.com.

A new blog called the Genomics Law Report went live today, promising to provide “news and analysis from the intersection of genomics, personalized medicine and the law.”  This blog will undoubtedly be a must for anyone interested in personal genetics.  Daniel MacArthur at Genetic Future has already provided a brief summary.

From the introductory post:

“…Robinson, Bradshaw & Hinson proudly announces the launch of the Genomics Law Report.  The Genomics Law Report focuses on the legal implications of important developments in the fields of genomics and personalized medicine — including key litigation, legislative, regulatory and policymaking activities — in order to facilitate understanding of the complicated and shifting legal landscape governing genomic and personalized medicine commerce and research.”

From today’s press release:

Posted via web from Blaine Bettinger’s Lifestream