The Genetic Genealogist

• 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.

ISOGG, the International Society of Genetic Genealogy, has a “Success Stories” page where it posts short summaries of just a few the many successes that genetic genealogy has helped people achieve.  Today I noticed that there are several new summaries regarding “Autosomal DNA Successes,” both of which were the result of 23andMe’s new Relative Finder (currently still in beta testing).

Relative Finder

As I recently wrote, Relative Finder is a feature at 23andMe that allows users to compare their autosomal DNA to the autosomal DNA of others to potentially find cousins.  This has long been done with Y-DNA and mtDNA, but this is one of the first times this has been done with autosomal DNA.

Success Story #1

The first success story is from someone who used Relative Finder to identify a huge number of potential cousins.  After connecting one of his or her potential 4th cousins, the individuals discovered that they have similar surnames from a certain location in common (in addition to DNA on chromosomes 3 and 10).  This individual also wisely noted that s/he now has “a good idea of the path that two of my DNA segments took through my pedigree to get to me.”  This is something I wrote about recently in “The Future of Genetic Genealogy – Tracing DNA To Individual Ancestors.”

Success Story #2 – A First?

The second success story is about two Relative Finder users who worked together to identify a line that they had in common, potentially identifying segments of DNA passed to them from a couple who were born in the 1730’s.  This is a very interesting result, and I wonder if it is the first time that genealogists have identified a segment of DNA that they inherited from distant autosomal ancestors (i.e. not their Y-DNA or mtDNA lines) outside of the medical realm.

Conclusion

I know I’ve mentioned this a great deal lately, but I again emphasize that geneticists and genealogists will be seeing much more of this type of success story in the future.

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.

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.

In a video available through CNBC, Linda Avey sits down to talk with Healthy Horizons about 23andMe.  The short video was originally aired today (7/24/09).

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.

On July 8th, Ancestry.com hosted a webinar called “Genetic Genealogy Made Easy.”  The webinar is now posted and can be accessed at any time.  One great thing about a webinar is that it can be multimedia; indeed, this webinar uses both slides and video.

The presentation is pretty basic, but a good source of information for people who are new to genetic genealogy.  The following topics are covered, according to the site:

- DNA testing for genealogy works–in easy terms.
- To understand and apply your results to grow your tree.
- Ancestry.com DNA testing can continue to pay off for years.
- Women can benefit from a paternal lineage test.
- To use Ancestry.com DNA features: Groups, Transfer to Tree, and Ancient Ancestry.

Ancestry.com is planning more advanced genetic genealogy webinars in the future.

What is interesting is that the last question from the audience addressed by the webinar regards using genetic genealogy by adoptees.  Whenever I give presentations, I almost invariably receive this question in one form or another.  Seems to be a very common question.

From today’s press release:

Posted via web from Blaine Bettinger’s Lifestream

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:

SALT LAKE CITY (May 26, 2009) – GeneTree and Sorenson Molecular Genealogy Foundation (SMGF) today announced a special offer to the tens of thousands of men who donated their Y-DNA samples and pedigree information to the non-profit SMGF’s genetic genealogy database. At a deeply discounted price, participants now may access their Y-DNA profiles through GeneTree and employ the site’s extensive tools, including the SMGF database, to search and connect with genetic relatives.

SMGF has been building the database-the world’s most diverse collection of genetic genealogy information-since 2000 through donation of DNA samples and four-generation genealogy questionnaires by people interested in helping the foundation succeed in its goal of connecting the human family through genetic genealogy. Until the launch of GeneTree in Oct. 2007, SMGF did not have a way to provide participants with their genetic profiles in a meaningful form. Now for $49.50, or about one-third of the typical price, SMGF participants can receive their Y-DNA profiles through GeneTree.

“We are delighted to be able to thank those who chose to help the SMGF database project,” said Matt Cupal, president and COO of GeneTree. “We think the easy-to-use and powerful genetic genealogy tools on GeneTree will help them get the most out of their DNA profiles and help them understand their own history within the larger human genetic story.”

Y-DNA is genetic material passed down exclusively from a father to sons. SMGF participants who submitted their mitochondrial DNA, passed down from a mother to each child, received a similar offer in March 2008, and may still unlock their mitochondrial DNA profile through GeneTree for $49.95.

“We believe this is the finest way we can express our appreciation to individuals who helped build the SMGF database into the foremost genetic genealogy collection of its type in the world,” said Dr. Scott Woodward, executive director of SMGF. “Collaboration with GeneTree allows us to provide contributors with their DNA profiles in a useful and confidential manner.”

Currently, the SMGF database contains more than 100,000 DNA samples and over 7.5 million corresponding genealogical records from participants in 170 nations throughout the world.

Instructions for obtaining SMGF DNA profiles for participation on GeneTree are available at www.genetree.com/dna/unlock_smgf. Approximately two weeks after receipt by GeneTree of the participant’s request, results will be available on the GeneTree Web site.

Beyond free basic membership, GeneTree offers 33-marker Y-DNA tests for $149 and 46-marker tests for $179. Enhanced maternal lineage mitochondrial DNA tests are $179.

About GeneTree
GeneTree (www.genetree.com) is mapping the world’s DNA using genetic genealogy. GeneTree’s Web site allows easy connection to genetic cousins, collaboration on family trees, and sharing of personal profiles and photos. GeneTree also provides the option for participants to integrate into their family history research their DNA profiles, through one of the world’s most respected DNA laboratories, for a scientific window into their ancestry and to find living relatives for whom no paper records exist. GeneTree users are linked to the world’s most extensive correlated genetic genealogy database.

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 free, publicly available 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.