The Genetic Genealogist

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Archive for the "DNA in the News" Category


The Genomics Law Report Addresses the ACCP’s Call for Regulation of DTC Genetic Tests

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).

Sorenson Molecular Genealogy Foundation First to Adopt Genetic Genealogy’s New Industry Standard for Reporting Y-DNA Profiles

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.

Using DNA to Explore the Scottish Roots of the Haley Family

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.”

Pathway Genomics Officially Launches

imageIn 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.

Genomics Law Report – A New Blog

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.”

Sorenson Molecular Genealogy Foundation to Protect DNA Samples Using Biomatrica’s Room Temperature Storage

From today’s press release:

Biomatrica today announced that the Sorenson Molecular Genealogy Foundation (SMGF) will use Biomatrica’s SampleMatrix room temperature storage technology to archive its DNA samples.

SMGF will use the SampleMatrix technology in place of ultra-low-temperature freezers for the long-term storage of all newly collected samples. In addition, SMGF will move its collection of previously archived samples from freezers to room temperature storage.

“SMGF has an extremely valuable collection of DNAs, and we have been very concerned about the long-term storage and preservation of the collection,” said Scott Woodward, executive director of the Sorenson Molecular Genealogy Foundation. “Biomatrica has developed a product that we feel addresses our concerns in a very practical, economical and secure way.”

According to the article, the technology is “based on extremophile biology in which organisms are able to survive long-term in a state of anhydrobiosis (life without water) and later be revived by rehydration.”  It works by “forming a thermostable barrier during the drying process to protect samples from degradation during storage at room temperature.”

Truly amazing stuff, and what a cost savings!

Posted via web from Blaine Bettinger’s Lifestream

“Can DNA tests help your genealogical inquiries?” in the Asheville Citizen-Times

An article appears in today’s Asheville Citizen-Times (here) about genetic genealogy. Although brief, the article summarizes the sciences behind Y-DNA and mtDNA testing, and focuses on the use of genetic genealogy to explore the “Clark” surname.

With the famous Thomas Jefferson-Sally Hemmings case, folks began to realize that DNA testing techniques could give answers and break down brick walls as never before.  While DNA will never replace standard research and primary documentation, it can be considered a tool to be used hand in hand with standard research.

via citizen-times.com and familybuilder

Posted via web from Blaine Bettinger’s Lifestream

A Critique of Genetic Ancestry Testing in Science Magazine

Gold StandardFive bioethicists have published a paper in today’s issue of Science – The Illusive Gold Standard in Genetic Ancestry Testing (paid subscription required) – calling for government regulation of genetic ancestry testing (aka genetic genealogy). There is an accompanying press release: “Stanford Bioethicist and Colleagues Call for Federal Regulation of Genetic Ancestry Testing” (another press release is available here).

Overall Thoughts

I highly respect the work of these authors, and I appreciate their efforts to educate the public about these issues. I do, however, wonder why the article was published in Science. The article mostly rehashes arguments found in a number of other articles (including from a very similar 2007 Science article (link) with some of the same authors) without adding any new research or supporting evidence. This is my greatest criticism of this and related articles – much of the hypothesis rests on anecdotal evidence without any corresponding research for support (such as objective social research with genetic ancestry testing customers).

What is different about this article, however, is that it very strongly promotes government regulation of genetic ancestry tests; indeed, this is the overarching purpose of the article. And this is perhaps one of the reasons that the article was accepted for publication: we are presently in a highly-charged atmosphere as a result of the interplay between DTC genetic testing and potential & existing government regulation.

Mutual Responsibility and Accountability

The authors state that one of the issues that emerges long before genetic ancestry tests are available is the collection of DNA samples used to create (and supplement, I suppose) an initial commercial database: “ethical questions about the collection and use of DNA samples must be resolved before researchers are permitted to sample many of the populations needed to approximate the full range of human genetic diversity.”

I agree that it is vital that any and all DNA collection & use from indigenous populations be constrained by clear and well-developed ethical standards. However, while the statement that “incomplete representation of human genetic diversity in existing databases” is a limitation of genetic ancestry testing is entirely accurate, the implication that all testing should await this approximation of completeness is not practical or tenable. Rather, entities doing genetic ancestry testing must continue to inform consumers about this limitation. Imposing a government-imposed definition of “completeness” of a database through regulation is clearly not the solution. Is there anyone on the planet today who can adequately describe what a database that would contain a complete or even approximate representation of human genetic diversity would look like? Certainly not, as research endeavors such as The Genographic Project are still working to describe human genetic diversity.

Finding Common Language

Interestingly, the authors state that “[t]he high stakes of genetic ancestry research require innovative approaches to dialogue, collaboration, and power-sharing between academia, industry, consumers, and community groups.” I think this is a reasonable approach, and one that has been proposed to me in the past by others in the field. The authors go on to state that:

“A first step may be joint creation of a vernacular that characterizes key concepts like probability, association, origin, and ancestry to help minimize variability that exists in how such concepts are understood across fields, communities, and governmental and commercial entities with different vantage points.”

The authors then discuss the term “origin” as an example of a term that is “not transparently or consistently defined.” Creating and enforcing any definition of this term could be problematic, a symptom of the very field in which it will be used. Terms such as “origin,” “ancestry,” “heritage,” and “genealogy” mean something different to each person. Indeed, a recent study has suggested that many customers of genetic ancestry testing adapt the results of the tests into their pre-established sense of self (which includes their personal definitions of origin, ancestry, and heritage). Again, the solution here (as the authors do seem to be suggesting) is education; each entity offering genetic ancestry testing should make the benefits and limitations of genetic genealogy clear.

Government Regulation

As I stated before, this article is the strongest proponent yet of increased governmental regulation of genetic ancestry testing. Yet, as I have previously argued it is education, not government regulation, that can most adequately address the issues the authors raise. For me, the “gold standard” of genetic ancestry testing is and always will be the education of consumers, not the regulation of testing companies. In furtherance of this belief, I have spent the last two years building this blog and associated works in order to help educate these consumers.

The authors conclude that government agencies are best suited to “discover common language and to identify best practices for presenting the limitations of current genomic technologies and the risks associated with over-extrapolating or misinterpreting genetic ancestry results.” The perceived need for regulation in this area necessarily relies on genetic exceptionalism, which holds that genetic information is fundamentally different from all other information about an individual. I’ve never been a believer of genetic exceptionalism, however. I suggest that the argument relies on genetic exceptionalism because the authors promote regulation of genetic ancestry testing, not of all genealogical research. Indeed, almost any type of genealogical research – including traditional paper record research and family interviews – inherently has “limitations” and suffers from the possibility of “over-extrapolation” or “misinterpretation”. Yet the answer here is clearly education, not government regulation of how the limitations of the supposed “facts” in great-great-aunt Maude’s birth certificate can be communicated to the public.

Instead of spending precious time enacting regulations that will do little to educate the public about genetic ancestry testing, let’s work together to increase the education of customers. Middle school and high school students need a stronger education in genetics in order to face the inevitable Genetic Future (see, for instance, the fantastic work of Harvard’s Personal Genetics Education Project), and adults require easily understandable resources available at their fingertips. This, not remote government regulation, will directly benefit consumers.

The Havasupai

The article also mentions researchers’ use of DNA samples from the Havasupai Tribe for various research projects despite the fact that individuals only consented to a study regarding diabetes (more info here). Although I am not familiar with either the law or the facts of this case, it is clear that there should be bright ethical guidelines for researchers to follow in order to prevent what the Tribe (and undoubtedly many others) obviously believes is a misuse of the samples.

However, with all due respect I question the inclusion of this issue in the article. The purpose of the article is to promote the use of government agencies to set industry guidelines (to “identify best practices for presenting the limitations of current genomic technologies and the risks associated with over-extrapolating or misinterpreting genetic ancestry results”). The Havasupai controversy, on the other hand, regards the collection and use of biological samples for research purposes. However, most if not all genetic ancestry testing companies either already have well-established proprietary databases or never engaged in the collection of biological samples from non-customers (instead forming a database from published data); other than The Genographic Project, I am unable to name a single genetic ancestry testing company that is or plans to obtain biological samples from non-customers for research (or any other) purposes. Indeed, even if government regulation of genetic ancestry companies had been established 10 years ago, I don’t think the Havasupai controversy would have been avoided.

Yet, tellingly, almost a third (30.7%) of the news release – about this paper discussing increased regulation of genetic ancestry testing – specifically highlights the very charged Havasupai issue. The issue feels out of place as the article is read, and while it is an example of the need for increased ethical guidelines regarding the collection of biological samples for research purposes, the fact that it does not support or even address the conclusion of the article leads me to question its inclusion.

Conclusion

As I wrote when the ASHG statement was released last year, government regulation in this field will not solve the issues raised by these ethicists (for the reasons stated above, among others).  The answer is consumer education, something that is the responsibility of both the consumer and the testing company.  Indeed, companies should continue to review and revise their customer education policies to ensure that the potential benefit and limitations of genetic ancestry testing are clearly understood by consumers before they purchase a test kit.

Family Tree DNA Discovers Y-DNA Signature That Might Represent the Prophet Mohammed

DNA 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:

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“You Can’t Handle the Truth” – an Article Arguing Against Increased Federal Regulation of DTC Genetic Testing

Alzheimer disease A recent article by Ronald Bailey in reasononline asks whether genetic tests actually need more federal regulation.  It’s probably clear that I strongly support the individual’s right to their own genetic information via DTC testing, but this viewpoint is rarely seen or endorsed in the press.  Bailey concludes:

“There may well be some inaccurate tests and there will certainly be people who mislead customers about the meaning of certain tests. But do we really need additional federal regulation to weed out bad actors? Most evidence suggests that the current tests are fairly accurate, and that customers are not being misled by the results that are reported. All new technologies involve a societal learning process in which some early adopters try it out, explain to others how it works, and find out its flaws—which newer innovators then fix.”

Accuracy of DTC Testing

The article also briefly discussed the accuracy of DTC testing (something I’ve covered here before – Accuracy of Large-Scale Genome Scanning Services):

“[The author] asked Princeton University molecular biologist Lee Silver via email how accurate the DTC genotype scanning tests are. “I ran an analysis on personal genome results obtained from 23andMe and DeCODE for me,” Silver replied. “There were about 300,000 data points that overlapped between the two tests. There was not a single data point (among 300,000) that was scored positive in one test and negative in the other.” Silver is satisfied with accuracy of such screening tests.”