15

The Genetic Mess in California – A Round-Up, and My Thoughts

On June 9, 2008, the California Department of Public Health sent cease and desist letters to 13 companies that offer genetic testing. According to the letters, the companies are in violation of certain sections of the Business and Professions Code of California, including offering “a clinical laboratory test directly to the consumer without a physician order” since such tests “must be ordered by a physician or surgeon” (according to these officials). Copies of the letters are available here. The companies receiving letters are:

  • 23andMe
  • CGC Genetics
  • deCODEme Genetics
  • DNA Traits
  • Gene Essence
  • HairDX LLC
  • Knome
  • Navigenics
  • New Hope Medical
  • Salugen
  • Sciona Inc
  • Smart Genetics
  • Suracell Inc

I’m entering this discussion late, although I’ve been watching with great interest. What I’ve noticed is that much of the discussion, both in the blogosphere and the media, is confusing or ignoring the fact that there are actually two questions involved here.

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5

Complete Neanderthal Genome Sequenced – Differs from CRS at 133 Positions

iStock_000003743546XSmall GenomeWeb Daily News published a story on Friday entitled “En route to Neandertal Genome, Researchers Analyze Its Complete Mitochondrial Genome” which revealed the results of recent Neanderthal mtDNA analysis.

On Thursday May 9th, Svante Pääbo spoke at the Biology of Genomes meeting at Cold Spring Harbor Laboratory. Pääbo’s group, along with 454 Life Sciences, is currently engaged in a project to sequence the Neanderthal genome. The researchers have been able to sequence the complete Neanderthal mtDNA genome with 35-fold coverage. The genome is approximately 16 kilobases long and differs from the CRS at 133 positions. From what I’ve been able to find online, it doesn’t appear that the actual sequencing results have been released to the public. Given current estimates of mtDNA mutation rates, the number of differences between human and Neanderthal mtDNA suggests that the branches diverged approximately 600,000 years ago.

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3

Press Release From The Newly-Created DNA Fund

Last week I received a press release announcing the creation of a non-profit organization to raise and disseminate funds to increase original research in genetic genealogy testing (some of which will undoubtedly be reported in the open-source Journal of Genetic Genealogy). The DNA Fund also has a blog, available here. Following is the press release:

SALIDA, CA – The DNA Fund, (www.dnafund.org), a new non-profit organization has been established to fund DNA testing scholarships and grants for ancestral DNA studies. Currently in Phase 1 of the Fund’s launch, testing monies will be raised through fundraising affiliates. Scheduled for Phase 2, the Fund will accept donations and in Phase 3, coordinate grants for DNA projects and studies.

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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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6

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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7

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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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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2

Genetic Genealogy on TV – Meeting David Wilson

MSNBC will air a documentary tomorrow evening about the journey of 28-year-old African American David Wilson as he discovers his genealogical roots. Wilson uses both traditional genealogical research as well as DNA testing to learn more about his ancestry. Along the way, Wilson meets another David Wilson, a white 62-year-old descendant of the slaveowners who owned the other’s ancestors. From the Meeting David Wilson website:

“Coinciding with the 40th anniversary of the assassination of civil rights leader Dr. Martin Luther King, Jr., MSNBC will premiere “Meeting David Wilson,” the remarkable and inspiring story of a young man’s reconciliation with his ancestors’ history as slaves. The world premiere of “Meeting David Wilson,” on April 11 at 9 p.m. ET will be hosted by “Today” Correspondent Tiki Barber and followed by a 90-minute live discussion of racial issues in America. The live event will be moderated by “NBC Nightly News” Anchor and Managing Editor Brian Williams and held at Howard University in Washington, D.C.”

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7

Navigenics Open For Business

Navigenics, a genome scanning company, officially launches their genome service today – called the “Navigenics Health Compass”, with a cocktail reception in NYC tonight at 6:00PM. Thomas Goetz of Epidemix writes an article in Wired today about some of the differences between Navigenics and other large-scale genome scanning companies.

The launch is also mentioned in an exclusive interview at Genetics and Health with Navigenics’ medical director, Dr. Michael Nierenberg. This piece is the first article in a seven article series, including the future article 6, which discusses some of my favorite things: “Privacy, insurance, GINA, and ethics.” I’ll be sure to link to that article when it comes out. The launch is also discussed over at ScienceRoll.

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