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DNAPrint Genomics and a New Roots Television Video

Megan Smolenyak Smolenyak recently wrote “I’m a Euro-Mutt!” about the results of her AncestrybyDNA EuropeanDNA 2.0 test (from DNAPrint Genomics). Megan found that the results of her test were both expected and surprising! From DNAPrint Genomics’ website:

DNAPrint® Genomics’ powerful new EuropeanDNA 2.0 product, further elucidates European sub-ancestry using 1,349 European Ancestry Informative Markers (SNP AIMs). This test reports a customer’s proportional basic continental European ancestry: Southeastern Europe (SEE – Armenian, Jewish, Italian and Greek), Iberian (IB -Spanish, Portuguese), Basque (BAS – Spanish/French Pyrenees border), Continental European (CE – German, Irish, English, Netherlands, French, Swiss and some Italian) and North Eastern European (NEE – Polish, Baltic, Swedish, Norwegian, Finnish, Russian) ancestry.

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Human mtDNA Diversity Before Migration Out of Africa

image Yesterday, a very interesting paper was published in the American Journal of Human Genetics by the Genographic Project Consortium entitled “The Dawn of Human Matrilineal Diversity.” The results of the study, which examined the 624 mtDNA genomes from sub-saharan Haplogroup L lineages, suggests that humanity once split into two small groups with one group in eastern Africa and the other in southern Africa, and that humanity bottlenecked into a relatively small number of individuals (as few as 2,000 based on results from a previous study). Note, as always, that these are hypotheses based upon the results of this and other studies, and will require further research to support or refute.

Two mtDNA Branches

The human mtDNA tree has two main branches, the L0 branch which includes individuals concentrated in southern and eastern Africa, and the L1’2’3’4’5’6′ branch (aka the L1’5 branch), which includes the entire remainder of humanity including non-Africans (see the figure to the left). Based upon the analysis of the 624 genomes, the researchers hypothesized that the L0 and L1’5 branches diverged into two small populations around 140,000 to 210,000 years ago, with one group settling in eastern Africa (the L1’5 branch) and the other settling in southern Africa (the L0 branch). Interestingly, the results also suggest that there was little to no intermingling of these branches for the next 50,000 to 100,000 years!

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GINA: An Update

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.”

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Finally, GINA Gets Her Day

iStock_000005432570XSmall On April 27, 2007, I wrote “GINA: A Primer“, which was an introduction to the Genetic Nondiscrimination Act. Today, nearly a year later, the bill will most likely be voted on and passed by the Senate, the last step before being handed over to President Bush to sign into law (which he has indicated that he will do). As I wrote last April:

“GINA aims to protect individuals in a variety of different areas. The legislation would prohibit access to genetic information by insurance companies and would prohibit insurance companies from discriminating against an applicant based on genetic information, the refusal to submit genetic information, or for have been genetically tested in the past. Additionally, the Act would prohibit employers from using or collecting genetic information to make employment decisions. The Act also establishes a Genetic Nondiscrimination Study Commission that is charged with reviewing new developments in the field of genetics and advising Congress.”

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Genetic Genealogy, Public Databases, and Criminals

The Washington Post has an article entitled “From DNA of Family, a Tool to Make Arrests” about using DNA obtained from family members to search DNA databases or identify relatives as criminals. Here is a summary of the issue from a recent Columbia Law review article available here (pdf):

For years, law enforcement personnel have compared DNA found at crime scenes with that of a convicted offender. Recently, a new technique has
begun to focus on the genetic similarity of biological relatives. Now, if a crime scene sample partially matches the DNA profile of a previous offender, law enforcement can investigate and possibly arrest that person’s family members. This process is called familial DNA testing and will significantly increase the amount of genetic information contained in the FBI’s Combined DNA Index System (CODIS), which consolidates local, state, and federal DNA databanks into a uniform body of data.

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The Spring 2008 Issue of the Journal of Genetic Genealogy

Yesterday the Spring 2008 Issue of the Journal of Genetic Genealogy was published online. As always, the journal and every article is completely FREE. Here is a listing of the articles in the current issue:

  • Editor’s Corner – A New Y Tree by Whit Athey
  • ‘Satiable Curiosity – Y-Chromosome and mtDNA Information from deCODEMe by Ann Turner
  • Genetic Structure of an Isolated Sub-Tribe of the Adi People of Arunachal Pradesh State in Northeast India: Isonymy Analysis and Selective Neutrality of Surname Distribution in Adi Panggi by Suvendu Maji and T. S. Vasulu
  • The Subclades of mtDNA Haplogroup J and Proposed Motifs for Assigning Control-Region Sequences into these Clades by Jim Logan
  • A New Subclade of Y Haplogroup J2b by T. Whit Athey and Bonnie E. Schrack
  • Where Did European Men Come From by Kalevi Wiik

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Tracing a 500-Year-Old Founder Mutation Using Genetic Genealogy

image In January I wrote about a study that traced a mutation in a single colon cancer gene to 1630. Today, researchers announced that a founder mutation in another gene, MSH2, has been traced to roughly 500 years ago (“Origins and Prevalence of the American Founder Mutation of MSH2” (pdf)).

MSH2 is a mismatch repair gene, and mutations in the gene results in Lynch syndrome, also known as hereditary nonpolypsis colorectal cancer. Lynch syndrome accounts for 2.8% of all colon cancers in the Western world, with 4,500 cases a year in the U.S. One specific mutation in MSH2, the deletion of exons 1 through 6, was named the American Founder Mutation (AFM) and was identified in nine families. Previously, research had suggested that the mutation in the MSH2 gene had been brought to Pennsylvania by German immigrants in the early 1700’s.

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TGG Rated 9.0 at Blogged

I recently received notification that The Genetic Genealogist has been rated a 9.0 at Blogged:

The Genetic Genealogist at Blogged

What is Blogged? From the website:

“Blogged.com is all about blog discovery. It’s a place for readers to discover interesting blogs and for authors to discover who their readers are. Blogged goes beyond being a traditional blog directory. We focus on providing tools for bloggers and readers alike. Through our database of over 200,000 blogs, readers can discover and explore new blogs. Through our user community, blog authors and their readers can communicate and interact directly with each other. Our blogs are reviewed, rated, and categorized by our editors, so you won’t have to experience the frustration of filtering through blogs that are either spam, outdated, or irrelevant. You’ll be able to find quality blogs that you would have unlikely found through a traditional blog search.”

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From Forbes: "States Crack Down On Online Gene Tests"

New York

Update: See the related story in GenomeWeb News (free sub. required).

Forbes.com published an article today entitled “States Crack Down On Online Gene Tests” that examines New York state’s response to the recent launch of direct-to-consumer (DTC) genetic testing services by companies such as 23andMe, deCODEme, SeqWright, and Navigenics, as well as the behind-the-scenes companies like Illumina and Affymetrix.

Unfortunately, the regulatory environment surrounding DTC genetic services is hazy at best. From the article:

“Over the last six months, New York State’s Department of Health has sent letters raising the specter of fines and jail time to six online gene-testing firms that offer consumers the ability to peer into their genome to assess their future risk of getting diseases such as cancer, heart disease and multiple sclerosis. Often, it turns out, the services offering these DNA deep-dives are doing so without the involvement of a doctor. That puts them on the wrong side of the law.”

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Essay Contest Reveals Misconceptions of High School Students in Genetics Content

The American Society of Human Genetics announced a press release out today about a study of student essays submitted as entries in the National DNA Day Essay Contest in 2006 and 2007. The ASHG’s education staff examined 500 of the 2,443 essays and found that 55.6% of the essays contained at least one “obvious” misconception, and 20.2% contained two or more misconceptions.

At first glance I was a little concerned about mining these essays – notably submitted by eager students to win a contest – for this type of information, but then I concluded that the authors of the essays must have assumed that they were being evaluated based on the accuracy of their statements. Additionally, the ASHG took careful steps to preserve anonymity.

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