The Genetic Genealogist

23andMe has been beta testing a new tool for comparing autosomal DNA results called “Relative Finder.” Although I was not one of the beta testers, it seems that this new tool will be of great use to genealogists. Roberta Estes has posted a nice summary of the Relative Finder tool at the “Searching for the Lost Colony DNA Blog.”

90% of Customers Likely to Find a Match!

Relative Finder compares your autosomal SNP results to the results of others in the 23andMe database to determine matches. While developing the tool, 23andMe discovered that in their dataset of “more than 5000 individuals with European ancestry,” 90% of individuals had at least one distant relative between 2nd and 8th degree cousins!

Other Uses

Beyond identifying distant relatives, the tool will potentially have many other uses. For example, one individual has already used SNP testing and comparison of 6 cousins to determine the approximate chromosomal location of an autosomal dominant hereditary condition!

The ASHG Abstract

Below is 23andMe’s abstract for the upcoming 2009 ASHG (American Society of Human Genetics) meeting regarding the Relative Finder tool:

Discovering Distant Relatives within a Diverse Set of Populations Using DNA Segments Identical by Descent.

L. Hon, B.M. Henn, J.M. Macpherson, N. Eriksson, A. Wojcicki, L. Avey, S. Saxonov, J.L. Mountain. 23andMe, Inc, Mountain View, CA.

“Close familial relationships, such a parent-offspring relationships, are inferred readily from genotype and allele frequency data for a limited number of single nucleotide polymorphisms (SNPs) or short tandem repeat (STR) polymorphisms. However, researchers have not focused on accurately inferring the degree of relationship between individuals who share a common ancestor 3-10 generations ago; such inference requires high density genome-wide information not available until recently. In order to characterize relatively distant relationships for a sample, we analyzed the sharing of DNA identical by descent (IBD) in a large database of self-selected individuals of European ancestry, including a subset identified as Ashkenazim. Individuals from more endogamous ethnic populations, such as the Ashkenazim, share on average more DNA identically by descent than do individuals of Asian ancestry or of European ancestry broadly defined. Extensive population level sharing of identical genomic segments complicates the prediction of relationship level for a pair of individuals since identical segments may reflect common ancestry older than the most recent ancestor for a pair of individuals in a pedigree. In order to understand the pattern of the observed population-level sharing, we simulated extended pedigrees using different populations to calculate the expected amounts of sharing for 1st through 10th cousins. Specifically we assessed the relationship between the length of the longest segment and the most recent common ancestor. From the simulations, we also determined bounds for predicted cousinships given a specific amount of segmental sharing. Using these bounds as a guide, we detected at least one distant relative, between 2nd-8th degree cousin, for 90% of individuals in our dataset of more than 5000 individuals with European ancestry. An even higher fraction of our Ashkenazi sample, 99%, had at least one distant relative between 2nd-7th degree cousinship in our dataset.”

Last week my Google alert for “genetic genealogy” went crazy, and it took me a few days to realize that Ancestry Magazine recently made all their archives available for free online.  Although I’m not sure how far back their archives go, there appears to be hundreds of genealogy articles on the site.

A quick search of “DNA” at the site, for instance, reveals MANY articles relating to genetic ancestry testing. This is a great resource for anyone interested in genetic genealogy.

I see that Schelly at Tracing the Tribe had the same Google alerts frenzy last week. As she notes, some of the articles are rather old, so be sure to check the dates before you read them; the information might require some updating!

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.

From a story in today’s Mormon Times:

The first rumblings about DNA and the Book of Mormon came about 10 years ago, according to Perego, a senior researcher at Sorenson Molecular Genealogy Foundation.Critics cobbled together data from a variety of early DNA studies and came to the unsurprising conclusion that the studies indicated an Asian origin for Native Americans.

This, the critics argued, proved that the Book of Mormon was false. They claimed that the book says the continent was empty and if it was empty, then all Native Americans should have Lehi’s Israelite DNA, not Asian DNA.

Ugo Perego, well-known in genetic genealogy circles, talks with the journalist about the compatibility of our current understanding of Native American origins and the Book of Mormon.  According to Perego, there are possibilities solutions to this apparent conundrum:

“Try to ask this question to a population geneticist: ‘Is it possible that a small family from Israel could have arrived in America, to a largely populated continent, and that no genetic evidence would survive after 2,600 years?’” Perego says. “Why don’t they ask that question? That is exactly the question they need to ask.”

Read the article to learn more.

The article is part 1 of a 4-part series.

Posted via web from Blaine Bettinger’s Lifestream

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.

The Social Security Death Index (SSDI) is a searchable database created from the U.S. Social Security Administration’s Death Master File, which contains the name and social security number of deceased persons reported to the Social Security Administration since roughly 1962.  In addition to being used by genealogists, the Death Master File and SSDI are used by financial firms and government agencies for various reasons such as preventing identity fraud.

A Genealogy Meme Using the SSDI

Michael Neill at RootDig has two posts – “Have You Searched for All Your Ancestors in the SSDI?” and “My in-laws in the SSDI” – that list his and his wife’s ancestors in the SSDI.  Michael has 7 ancestors, while his wife has 6.

This led me to wonder how many ancestors I have in the SSDI, and a very brief search led me to conclude that I currently have a total of 8:

1. Theodore LaBounty 1927-1983
2. Jane (Garcia) LaBounty 1931-1984
3. Theodore LaBounty 1903-1963
4. Goldiah (Blanchard) LaBounty 1906-1996
5. Roy Bettinger 1916-1975
6. Marley (Johnson) Snell 1889-1983
7. Victor Mullin 1901-1972
8. Clara (Fitzgerald) Mullin 1907-1997

Eventually I will have a total of 11 ancestors in the SSDI, but my parents and a grandparent are still, thankfully, living.  My wife also has a total of 8 ancestors in the SSDI:

1. Harlon Conger 1921-2005
2. Lois (Finney) Conger 1891-1975
3. John Alden 1900-1971
4. Margaret (Wolford) Alden 1902-1991
5. Inez Simmons 1891-1979
6. Albert Bacon 1895-1963
7. Guy Simmons 1921-1989
8. Margaret (Bacon) Simmons 1929-2007

Other Questions

Out of your ancestors in the SSDI, who had the earliest date of birth?  Mine is Marley (Johnson) Snell who was born in 1889, and my wife’s is a tie between Lois (Finney) Conger and Inez Simmons, both born in 1891.

How many of these ancestors did you meet (whether you remember it or not)?  I met 5 of my 8 ancestors in the SSDI, and my wife met 4 of hers.

How many ancestors do you have in the SSDI?

Trends in Genetics has an article by Turi E. King and Mark A. Jobling from the University of Leicester highlighting Y-DNA genetic genealogy.  Specifically, the article – “What’s in a name? Y chromosomes, surnames and the genetic genealogy revolution” – looks at the relationship between surnames and Y-DNA genetics.  Dr. King and Dr. Jobling have previously conducted a great deal of research in this area (see here and here, for example).

The article is a review of this area and contains some interesting information, including a section regarding “Genetic genealogy and the rise of recreational genetics.”

Genetic genealogists recognized as making genuine contributions to the field:

In the article, the authors note that genetic genealogists are making discoveries in this field:

“Genetic genealogy enthusiasts often display an impressive level of knowledge about aspects of molecular evolution, population genetics and statistics; some of this is evinced in the quarterly online Journal of Genetic Genealogy (www.jogg.info). Although it lacks the standard scientific peer-review system of traditional journals, it is nonetheless attracting academic geneticists among its authors and is an interesting model for public involvement in scientific publication. Other resources for genetic genealogy are listed in Box 3. Thanks to the advances in DNA technology and the power of the internet, genetics is now joining astronomy as a science in which amateurs can make useful discoveries.”

From the abstract:

Heritable surnames are highly diverse cultural markers of coancestry in human populations. A patrilineal surname is inherited in the same way as the non-recombining region of the Y chromosome and there should, therefore, be a correlation between the two. Studies of Y haplotypes within surnames, mostly of the British Isles, reveal high levels of coancestry among surname cohorts and the influence of confounding factors, including multiple founders for names, non-paternities and genetic drift. Combining molecular genetics and surname analysis illuminates population structure and history, has potential applications in forensic studies and, in the form of ‘genetic genealogy’, is an area of rapidly growing interest for the public.

HT: Ugo Perego

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.

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.