The Genetic Genealogist

1:25PM EST: Senator Olympia Snowe is currently on the floor of the Senate speaking about GINA (see it live on C-SPAN 2). And yes, I realize that live-blogging C-SPAN coverage is dangerously boring, but I can’t help myself!

3:00PM EST: I just received a press release from the Genetics & Public Policy Center that GINA passed the Senate 95-0:

The Senate today passed the Genetic Information Nondiscrimination Act (GINA), approving by unanimous consent of 95-0 an amended version of H.R. 493, which passed the House April 25, 2007 by a vote of 420-3. The House is expected to take up the measure again quickly before sending it to President Bush to sign the measure into law.

“After a very long wait, Americans can now be confident that their genetic information cannot be used by health insurers or employers in harmful or hurtful ways,” says Kathy Hudson, director of the Genetics and Public Policy Center, established at Johns Hopkins University by The Pew Charitable Trusts. “Our challenge now is to make sure that doctors and patients are aware of these new protections so that fear of discrimination never again stands in the way of a decision to take a genetic test that could save a life.”

The legislation, when signed, will fulfill the longstanding agreement among American citizens and politicians that protection from genetic discrimination should be clear and consistent, Hudson explains. Until now, individuals’ genetic information has been protected only by a largely untested patchwork of state and federal regulations. Ninety-two percent of Americans are concerned that results of a genetic test could be used in ways that are harmful to the person.

Moreover, scientists can now in good conscience tell patients and research participants that their genetic information is protected against misuse by health insurers and employers. Linking gene variants to health outcomes often requires studies involving large numbers of people, but scientists report that potential subjects are deterred by the fear that their information could be used against them by employers or insurers. In a survey of more than 4000 people conducted earlier this year, for example, the Center found that when considering whether or not to participate in genetics research, 93 percent of respondents said it was important that it be “illegal for insurers or employers to get my information.”

In addition to impeding research that would help to bring about the much-heralded era of personalized medicine, the threat of discrimination affects individual patients who could benefit from genetic testing have sometimes foregone it out of concern over possible repercussions. When people opt not to be tested, they lose the opportunity to seek monitoring and preventive care to avoid conditions for which they are at higher risk. Passage of GINA means that Americans will no longer have to make the trade-off between genetic privacy and appropriate health care.

The Senate unanimously passed versions of GINA in 2003 and 2005, but in both years the bill stalled in committee in the House. Last year, however, the House passed the measure quickly and today, the Senate for a third time expressed its commitment to nondiscrimination.

How much do you know about genetic genealogy testing? Take The Genetic Genealogist’s quiz!

The International Society of Genetic Genealogy (ISOGG) has just launched a new newsletter. The first edition, March 2008, is available here. This edition discusses GINA, a DNA Success Story by Shoshone, a segment called “The Armchair Geneticist: Where Hobby Produces Science”, What’s New in ISOGG, and a Featured DNA Project.

The newsletter is well-written and has some great graphics, so be sure to subscribe to this FREE newsletter (see the bottom of the newsletter for subscription information).

I often get emails from people who are new to genetic genealogy asking questions about their newly-received DNA testing results. They are unsure about about what the results mean, how to find more information, or what to do next. I also see people ask these questions in all of the DNA forums and mailing lists that I subscribe to. Although I do my best to help the people that email me, I often wish there was more I could do.

In an attempt to assist people with the interpretation of their genetic genealogy testing results, I’ve written an eBook that takes the reader step-by-step through an analysis of their Y-DNA or mtDNA results, including estimating a haplogroup and sub-clade from testing results, finding resources to learn more about particular haplogroups, and finding haplogroup and haplotype matches, among many other topics. Here is the Table of Contents from the 28-page eBook:

Chapter 1: What Is (And Isn’t) Genetic Genealogy?
Chapter 2: How Do I Interpret My Y-DNA Results?
Chapter 3: How Do I Interpret My mtDNA Results?
Chapter 4: Monitoring the Field of Genetic Genealogy

I’m offering this eBook for free to anyone that might be interested in interpreting the results of their genetic genealogy test. And please feel free to share this eBook with your friends, mailing list, or anyone else. Without further ado:

I’ve spent many hours over the past few months working on this eBook, and I hope that you find it helpful in your own genetic genealogy journey. If you find anything that might need correction, or have any suggestions for future editions, please feel free to email me. And check back often for updates to this eBook. If you find the eBook helpful, please consider subscribing to my blog for updates and future releases.

With the popular African American Lives series on PBS and numerous news stories and magazine columns, Black History Month often results in increased attention to the genealogy and genetic history of African Americans. I saw a similar increased interest in genetic genealogy last February as well.

The Multiracial Roots of Americans

Diverse has an article entitled “More Americans Are Discovering Their Multiracial Roots.” The article discusses traditional genealogical research, then mentions genetic genealogy – particularly automosal testing:

“One of the more fascinating developments with the new genealogy is the extent to which DNA testing is revealing the multi-racial ancestry of Americans. While there’s some controversy about the claims of DNA testing firms as to how accurately they can match individuals to ancestors from specific communities and ethnic groups, there’s a consensus that proper testing can roughly specify a person’s relative mix of his or her ancestors’ geographic origins.”

The Pursuit of Happyness

Another great article is in Medill Reports, “DNA Traces African Past.” Christopher Gardner, the real-life story behind “The Pursuit of Happyness,” was recently given the results of an mtDNA analysis and genealogical study by African Ancestry. According to the analysis, Gardner’s mtDNA likely originated in Sierra Leone, and he had relatives aboard the Amistad slave ship (although how they made this connection is unclear). The article states:

Gardner left the luncheon with a smile on his face. He said he needed time to “take in” his newfound information. “This is so overwhelming,” Gardner said. “It’s something that I want to encourage more people to do, especially African-Americans.”

The tests offered by African Ancestry (and the Kittles-Gates controversy) were also discussed in the cover story to N’DIGO Online, “African Roots? Test Your DNA!”

Re-Root Family Trees

The Daily Advertiser in Lafayette, LA has “Black History Month: Records help re-root family trees; see photo gallery from museum.” Earl Gates, president of the Lafayette Genealogical Society, presented a workshop on African-American genealogy this month and recommended that “genetic testing should be used as a tool and not proof of origins beyond a reasonable doubt.” Great advice.

As I was reading through the GENEALOGY-DNA list from Rootsweb this morning, I came across a great question about the frequency of mutation of mitochondrial DNA (mtDNA).

The listmember asks “I am wondering if anyone would know the odds of having a mutation between my brother and me in our mtDNA. Marker 16163 is G for one of us and A for the other…” This is a great question, and one that I’ve been asked as well.

In response, Ann Turner writes “The mutation rate hasn’t been studied in the detail I’d like to see. The largest study for the hypervariable regions was based on deep-rooting pedigrees from Iceland. They found 3 mutations out of 705 transmission events.”

The study, available here (pdf, HT: Ann Turner) was conducted through deCODE Genetics and Oxford University. They used 26 Icelandic ancestral trees to identify maternally-related individuals, and sequenced 272 mtDNA control regions representing a total of 705 transmission events. The researchers found a total of three mutations, resulting in a mutation rate of 0.0043 per generation, or 0.32/site/1 million years. A previous study (Parsons et al., 15 Nature Genetics 363 1997) found a total of 10 mutations in 327 transmission events for a frequency of 2.5/site/1 million years, and yet another study found 2 mutations in 81 transmissions for a rate of 0.75/site/1 million years (Howell et al., 59 Am J Hum Genet 501). The huge differences in these numbers suggests that much more research needs to be done, probably with a much larger dataset. If I had unlimited funds, I would also be interested to see if there are different mutation rates among haplogroups, as well as a number of other factors.

Another great thing about the deCODE Genetics/Oxford study is that it almost completely negated the effects of somatic mutations in mtDNA. Somatic mutations occur in non-reproductive cells and are not passed on to the next generation (essentially a dead-end stop for these mutations). Only “germ line” mutations are passed on to the next generation, and were the focus of this particular study.

If you aren’t already a subscriber or a reader of the GENEALOGY-DNA list, I suggest that you join or periodically peruse the archives (which are conveniently arranged by month and then by discussion). Some of the discussion can be a little complicated (i.e. heavy on the science), but there is always something interesting under discussion.

And don’t forget about my one-year blogging anniversary giveaway – you could win a FREE genetic genealogy test! Contest rules here. There have only been about a total of 50 entries, so your chances are still very good. I haven’t received many emails (my email is blaine_5 at hotmail.com) with the rss-only secret word (below), and it’s a great way to get two free entries. Good luck!

Although the world of genetic genealogy has slowed from the furor of November and December 2007, there is still plenty of discussion and consideration going on around the blogosphere.

First, Ann Turner , co-author of “Trace Your Roots With DNA” and moderator founder of the terrific Genealogy-DNA list has experimented with both deCODEme and 23andMe. Although she is still analyzing the results, she has a short write-up of deCODEme’s graphic presentations for comparing genomes (Word document here). The deCODEme comparison tool allows users to compare the degree of similarity between genomes, as long as the user has permission to compare. For those without a permissible genome to compare to, deCODEme provides reference samples from about 50 different populations. Ann points out that “it would be really interesting to hear if anybody is testing a number of close or distant relatives,” as their genome comparisons would be especially relevant.  Update: A revised version of Ann’s document with comparisons to more individuals is available here (zip file).

Jason Bobe at the Personal Genome writes “50 Million Personal Genome Sequences by 2015?” Although this post is not specifically about genetic genealogy, 50 million genomes (a substantial fraction of which will hopefully be available for scientific analysis) will impact many areas of life, including genetic genealogy (as we saw with the recent colon cancer study). Jason even agrees in the comments that genetic genealogy may actually be a driving force behind large-scale genome sequencing.

Genomeboy writes the “Quasi-official Yuletide PGP Update.” The PGP is the Personal Genome Project, which I have written about before. Lots of interesting news about the PGP, for those who are following the project’s developments. I know I am. I’m still debating whether or not to volunteer for their scale-up project to analyze 100,000 genomes.

The mitochondrial genome continues to reveal its many uses, aside from genetic genealogy (although they’re all related – no pun intended!). A new paper (available here by subscription, a great summary at henry) uses 357 mtDNA coding region sequences to hypothesize about the size of the human population through time across eight major geographic regions. According to the authors, the study’s findings “not only support the use of mtDNA data for estimating human population size but also provide a unique picture of human prehistory and demonstrate the importance of Southern Asia to our recent evolutionary past.”

Megan Smolenyak mentions the great new resource available through the ISOGG (International Society of Genetic Genealogy. Many DNA project leaders (myself included) are always looking for new ways to recruit members, and the new DNA Project Communication Methods Comparison should come in very handy. It presents examples of communication methods and lists some of the pros and cons of each.

The DNA Ancestry Blog asks, “Is It Always Better To Purchase The Highest Marker Test?” For the newbies, Y-DNA tests typically analyze anywhere from 12 to 67 markers, and deciding which one to purchase can be a difficult decision.

Dienkes’ Anthropology Blog has a series of posts about mtDNA and Y-DNA in different populations. Although I have to admit that I haven’t read them all, I’m sure that each one of them contains a tidbit of information that would be of interest to genetic genealogists. See “Mitochondrial DNA haplogroup diversity in Basques: A reassessment based on HVI and HVII polymorphisms,” “Contrasting Signatures of Population Growth for Mitochondrial DNA and Y Chromosomes among Human Populations in Africa,” “Characterization of mtDNA haplogroups in 14 Mexican indigenous populations,” and “Tracing Human Migrations with Y chromosomes and mtDNA (new Underhill/Kivisild paper).” The last paper has already generated 40 comments to that post.

bbgm writes about “Your personal health: The internet and privacy.” Singh strongly opposes the use of genotype to deny a person health insurance or other services, but argues that personal genome technology should be regulated by the market. He also concludes that the role of privacy advocates should be to educate the public (a point that I have made here at TGG a number of times).

And Hsien at Eye On DNA writes about the “American Society of Human Genetics (ASHG) Statement on Direct-to-Consumer Genetic Testing.” Although the statement was aimed at DTC genetic testing in Obstetrics & Gynecology, all of the topics involved are applicable to DTC personal genomic analysis as well. Look for LOTS more of this in 2008!

Last but not least, don’t forget about my one-year anniversary giveaway – you could win a FREE genetic genealogy test! Contest rules here.

Genealogists spend many of their days (and much of their money!) tracking the history of their ancestors. They hunt through ancient records to elucidate even the smallest clue as to some facet of their ancestors’ lives. Since the majority of genetic genealogists started their journey as traditional genealogists, it is only natural that they enjoy record-keeping and tracking as well.

The DNA Genealogy Timeline is a free public resource maintained by Georgia K. Bopp and hosted by rootsweb.com. The timeline attempts to track the significant developments associated with genetic genealogy. It begins with “Before 1980″ and was updated most recently as of October 2007.

What immediately stands out is that genetic genealogy has been around much longer than people realize, especially given the recent media attention. I began my exploration of genetic genealogy in 2003, but by 2000 there were already as many as 4 surname projects begun by hobbyists! As of September 2007, one company (Family Tree DNA) had over 4,200 surname projects that contained more than 66,000 surnames. There are even more surname projects hosted by other companies, including Heritage DNA.

The timeline also shows that genetic genealogy was first developed by geneticists and anthropologists to analyze a wide variety of problems facing researchers. The technology was later embraced by genealogists who saw that it could be used to answer some of the problems faced by other genealogists.

As the introduction states:

“This Timeline began when I could not find an informal context – a simple history – to use when called upon to explain the new field of DNA and genealogy to those who knew less about it than I (a beginner in October 2002 – and not a scientist). This contains items I’ve found as well as contributions by others, primarily Ann P. Turner and participants of the RootsWeb GENEALOGY-DNA discussion list and members of the ISOGG community.“

This is a great resource, and I’m thankful that Ms. Bopp has made it freely available to all. The site mentions that corrections and additions to the timeline are welcome.

If you’re thinking about jumping into the field of genetic testing (whether for genetic genealogy or any other form of genetic test), you should be sure to do some research first. The results of any genetic test are incredibly personal, and can potentially have a huge impact. As a result, the decision to undergo testing should only be made after doing some vital research.

Luckily, a fellow DNA Network blogger has written a post that will help you do this important pre-testing research. Hsien at Eye on DNA has written “How to Prepare Yourself for a Genetic Test.” Hsien provides the following advice:

“Although you can’t change your DNA, it is possible to prep yourself for a DNA test just as it’s possible to prep yourself for a driving test. It is critically important that anyone undergoing DNA testing learn as much as they can about the results they can expect to receive, the interpretation of these results, and the impact results may have on their life choices.”

She then lists and describes 5 different things you can do to prepare yourself for genetic testing. I highly recommend this post to anyone who is thinking about buying a test.

I honestly don’t know what to do with this next article. Meredith F. Small Ph.D., an anthropologist at Cornell University, wrote a brief article at LiveScience entitled “DNA Kits: Secrets of Your Past or Scientific Scam?” Dr. Small’s article is largely a comment on the article that appeared earlier this fall in Science, “The Science and Business of Genetic Ancestry Testing” (I provided an analysis of the article here at TGG).

According to Dr. Small:

“[The quest for identity] also leads unwary seekers of the past right into the hands of scam artists who claim they can trace anyone’s DNA back to its source.”

The sentence is extremely misleading:

First – a scam artist is by definition a person who engages in a “fraudulent business scheme.” Although genetic genealogy can be controversial, I’ve never heard a single customer accuse a company of running a scam. To the best of my knowledge, these testing companies are using the best science available to test DNA and compare results to their databases. Are physicians running a scam if they use open-heart surgery to fix a heart, rather than a simple pill that will be invented in 5 years? All technology is based on the best developed science right now. A company might have a limited database or only test a limited number of markers, but this does not qualify them as running a “scam.”

Second – The sentence also implies that genetic genealogy companies promise too much, and that genetic genealogists are unable to decipher the limitations themselves. As my readers might remember I discussed this assumption here. Most genetic genealogists understand and embrace the limitations of genetic genealogy, and also work to help others understand that difference. More can be done, and many are working to make that happen.

Similar sentences include “claims that this analysis will tell you much about where you came from are downright fraudulent, anthropologist Deborah Bolnick of the University of Texas at Austin and 14 co-authors recently reported,” and “Instead of tracing our genetic past, what we get is a scientific scam”

I think one of the major problems of this article is that the author or the editor doesn’t seem to the understand the underlying science. There is a MAJOR difference between autosomal testing and mtDNA or Y-DNA testing. This includes the science behind the test, and the science behind the interpretation of results. For instance, the article includes the following sentence:

“But, [anthropologist Jonathan] Marks points out, these companies are preying on the public because they simply don”t have enough comparative information to pinpoint a gene on a world map.”

For all you genetic genealogy newbies out there, there isn’t a test on the market that attempts to “pinpoint a gene.” Dr. Small fails to establish any line between autosomal testing and mtDNA or Y-DNA testing:

Some autosomal testing does attempt to identify the approximate predominate location of certain DNA markers (SNPs), but genetic genealogy companies do not sequences genes (other than in the full mtDNA test). And contrary to the implication of the article, these companies attempt to give very broad locations, such as “Northern Europe”, or “Asia”, not a specific town or county. Autosomal analysis is based on peer-reviewed science, the best we currently have available. It is true that there will be MUCH better data in 5 years or 10 years, but that doesn’t mean that using today’s science is a “scam.”

As for Y-DNA or mtDNA tests, the results are most often used to place the tested individual’s haplotype into a specific haplogroup. The approximate origin of all haplogroups has been established by peer-reviewed science. There are a few companies that use that haplotype data to identify a potential source of the mtDNA, for example. Again, that identification is based on peer-reviewed science and proprietary databases. Additionally, most genetic genealogists are aware of the limitations.

Perpetuating the mistaken scientific understanding, along comes the most egregious statement in the entire article:

“More insidious, these companies pretend to trace your unique ancestry through mitochondrial DNA, but that’s simply not possible. A few hundred years, a few generations, and every person’s history is a genetic mishmash. One little gene isn’t going to inform anybody about anything.”

It is obvious that Dr. Small either does not understand the underlying science, or is completely glossing over it. For the newbies, mtDNA is passed on almost always completely unchanged from mother to child. Every once in a great great while, that mtDNA changes in a very small way (that is, it gains a mutation). It does not “mishmash” with other mtDNA.

The mtDNA I inherited from my mother was inherited through an unbroken line of women until it ended with me. Employing genetic genealogy, I can trace my “unique ancestry through mitochondrial DNA.” I belong to Haplogroup A, which means that my maternal line crossed the Bering Strait thousands of years ago and settled in Central America. This is not conjecture, and I was not “scammed.” I used peer-reviewed science to come to that conclusion.

Now I confess that the mtDNA test only told me about a TINY percentage of my genetic heritage, but it was an exponential growth of information compared to what I had previously, which was nothing. And note, of course, that assignment of mtDNA into a specific haplogroup is based on single nucleotide markers, NOT on the sequencing of a gene.

The same holds true for Y-DNA testing. Although the markers used for comparative analysis appear to mutate somewhat more rapidly than mtDNA, Y-DNA is still passed largely unchanged from father to son.

And I felt that the concluding paragraph was dismissive:

“If you want to know who you are, look in the mirror. Written on your face is countless generations that have survived to reproduce, and the only thing you can realistically do at this point is thank them and then move forward.”

Genetic genealogy is a valuable part of my life. Although it doesn’t define who I am, it is a part of my identity. Attempting to learn more about myself and my ancestors through my genetic makeup has been a valid and rewarding endeavor. And the current field of genetic genealogy is only at the tip of the iceberg – so far we’ve been looking at a few random SNPs in our genome. Wait until science gets ahold of my entire genome.

P.S. -I will be sure to email Dr. Small about this post, so that she can respond to my criticisms.