14

Accuracy of Large-Scale Genome Scanning Services

Although the genome scanning services offered by companies such as 23andMe, deCODEme, and SeqWright have been front and center in the press the last few weeks, I’m sure that the following information will not be included in any of the reports.

Comparisons

Two different sources have concluded that the scanning service offered by 23andMe and deCODEme, who use different types of Illumina SNP Chips, are highly reproducible. In January 2008, Ann Turner compared the results of testing at deCODEme and 23andMe, and concluded that of the 560,163 SNPs that overlapped and had a “call” (meaning there was a measurable result), they agreed on 560,128 and disagreed on 35. Ann wrote in January:

In all of [the disagreed calls], one company would make a homozygous call while the other company made a heterozygous call – there were no cases where they made a completely discordant call. All in all, I’d say that is pretty impressive.

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9

Kwäday Dän Ts’ìnchi – "Long-Ago Person Found"

image Around the year 1700, a relatively healthy young hunter was walking along a glacier in land that would one day be British Columbia in Canada. He wore a robe of 95 animal skins, perhaps gopher or squirrel, stitched together with sinew, and carried a walking stick, iron-blade knife, and spear thrower. For some reason, the young man, aged 17 to 22, died on the glacier and was quickly incorporated into the ice. There he remained, frozen, for the next 300 years.

In August 1999, three hikers noticed a walking stick, fur, and bone lying on a melting glacier (60′ N 138′ W). The young hunter, renamed Kwäday Dän Ts’ìnchi in the Southern Tutchone language of the Champagne and Aishihik First Nations, was removed by scientists for analysis (see the NY Times article, and the Journal of Canadian Archaeology article). From an article in the Sydney Morning Herald:

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8

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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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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6

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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9

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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ThinkGenealogy Presents "Are You Smarter than a Grade School Genealogist?"

ThinkGenealogy introduces episode 1 of “Are You Smarter than a Grade School Genealogist?“: “Match your genealogy knowledge against a grade schooler to determine: Are You Smarter than a Grade School Genealogist? In this episode, Nathan, a 4th grader from Arizona introduces DNA for the genealogist.” The episode is just over 4 minutes long and is a great introduction to genetic genealogy.

11

DNA Testing of New York’s New Governor David Paterson

As of Monday the 17th of March, David Paterson will be the Governor of New York State.  Lt. Gov. Paterson recently sat down with Susan Arbetter of WHMT’s NYNOW to discuss the results of his genetic genealogy test results.  Paterson is probably the first governor in the United States to have undergone genetic genealogy testing, and might be the highest government official to do so and then speak openly about it.  These videos are very enjoyable, and it’s interesting to learn more about the future Governor.

In the first segment, Arbetter and Paterson discuss some of Paterson’s genealogy.  They also discuss Paterson’s Y-DNA, which is of European origin.  Arbetter writes on her blog: "On the Lt. Governor’s paternal side, like almost 25% of all African Americans, he’s got white progenitors from England, Ireland and Scotland."

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1

Links From The Genetic Genealogist – October 31, 2007

In order to clean out posts I’ve been saving in Google Reader (does anyone else keep posts in Reader until you’ve blogged about them?), I decided to have a potpourri day. The following are links to interesting articles around the blogosphere. And Happy Halloween!

Pedro at Public Rambling has The Fortune Cookie Genome, a ‘science fiction’ post about picking up the results of his whole genome scan from his genetic advisor. Of course, it’s only science ‘fiction’ until it’s science ‘reality’!

The Women’s Bioethic Project has an article about DNA Testing Without Consent, which asks whether there should be a ‘reverse’ statute of limitations for testing DNA from famous dead people. The article was written in response to a recent story in Parade. I talked about this briefly back in August (see “DNA From the Dead“), and I’m working on a post about “Discarded DNA and the Constitution”, so stick around. HT: Eye on DNA.

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17

10 DNA Testing Myths Busted

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1.Genetic genealogy is only for hardcore genealogists.

Wrong!If you’ve ever wondered about the origins of your DNA, or about your direct paternal or maternal ancestral line, then genetic genealogy might be an interesting way to learn more.Although DNA testing of a single line, such as through an mtDNA test, will only examine one ancestor out of 1024 potential ancestors at 10 generations ago, this is a 100% improvement over 0 ancestors out of 1024.If you add your father’s Y-DNA, this is a 200% improvement.Now add your mother’s mtDNA, and so on.However, with this in mind, please note the next myth:

2.I’m going to send in my DNA sample and get back my entire family tree.

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