The Genetic Genealogist

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.”

Unclear Regulations

I’m still not convinced. I recently wrote an article that reviewed New York’s statutes and regulations regarding DTC testing, and it is far from clear. Additionally, there is almost an entire lack of case law to help interpret these statutes. Ultimately it is a question of statutory interpretation and legislative intent. What did the original drafters of these regulations intend the laws to do, or to protect? How should these laws be interpreted today? These are difficult questions without clear answers, and thus will be the subject of much debate in the near future.

P.S. – I am currently working to find a journal in which to publish my article, so stay tuned for my input on this very controversial topic!

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.

The panel concluded that “misconceptions about genetics remain prevalent in U.S. science classrooms”, and included information about using the findings to improve genetics education. I highly recommend reading the entire paper, available for free from the ASHG and Genetics: “Essay Contest Reveals Misconceptions of High School Students in Genetics Content.” From the press release:

“The misconception most frequently identified in the researchers’ analysis of student essays was broadly defined into the category of “genetic technologies” (17.2%), these responses displayed incomplete understanding of the complexity of scientific research, including biotechnology and genetic engineering. Another common theme identified in the analysis revealed that students did not fully understand concepts related to heredity and patterns of inheritance (14%); these essays reflected students’ belief that single genes are the cause of traits and inherited diseases. In actuality, even in cases of simple inheritance, multiple genetic and/or environmental factors often play a role in the expression of a trait or disease.”

The paper includes some interesting examples of misconceptions, such as the following quote from a student’s essay:

‘‘One study showed that chemical dependency skips a generation. This would make the gene for chemical dependency recessive. This means that if a psychiatric geneticist would make a Punnett square for two parents whose parents had chemical dependency, the Punnett square would say that 3 out of 4 of their children would be chemically dependant.’’

The authors of the study respond with: “Chemical dependency is a complex trait that cannot be explained by a simple, monohybrid Punnett square cross.”

Everyone remembers the “big B” “little b” Mendelian crosses of things like eye color in biology class. But in today’s world of genetics, teaching this simplistic view of genetics, especially in high school (which is really just a basic introduction to genetics) might be too confusing. What do you think?

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.

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 40^th 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.”

The younger David Wilson also undergoes DNA testing in hopes to learn more about his ancestry:

“Curious to learn if they have more than a name in common, David tests his DNA. One of the results of this test identifies his African origins. Once this match is made, the lab provides him with a name and location of an African ethnic group and he travels back to Africa to complete his journey.”

To learn more, there is the official Meeting David Wilson Blog, an article on MSNBC, an interesting downloadable press kit (pdf) with a synopsis and pictures (pictures also available online here), other videos. And finally, here is the YouTube trailer:

HT: The Genealogue, and Megan’s Roots World.

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

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.

For more information:

• ThinkGene – Navigenics Launches Whole-Genome Scan
• PRNewsWire – Navigenics’ Genome Analysis Used In Research Trial on the Impact of Providing Genetic Risk Assessments
• The New York Sun – SoHo Agenda: Buy a New Suit, Then Stop in For Genetic Testing (according to the article, Navigenics is renting a “storefront at 76 Greene St. for 10 days” to “drum up business by hosting panel discussions on genetics and running other health programs.”
• Wall Street Journal – Genetic Testing Firm to Disclose Data Standards

Genetic testing has once again come under the microscope, triggered by an article in the journal Science: “A Case Study of Personalized Medicine.”

In my opinion, adding to the conversation about genetic testing is always a good thing.

That being said, my biggest complaint with many of these articles (especially in the popular media) is that they tend to lump together every test that examines DNA. There are different types of genetic testing with different levels of quality control, interpretation, etc. The results, scientific background, and effects of tests offered by large-scale genome scanning companies, clinical entities, direct-to-consumer companies, and pharmacogenetic companies are not the same. When dealing with a readership that does not have a background in genetics (which is probably 99% of the readership), the media should take extra care to note these differences. Lumping every DNA test together does little to properly educate the public.

Also unclear from almost every article is how genetic genealogy fits into the conversation. Based on what I read online and in the media, I still get the impression that most people are either unaware of genetic genealogy, or fail to understand the (20+ years of) science behind it.

Here is a round-up of the discussion triggered by the article:

• Newsweek – Beware Genetic Snake Oil
• Genelex – Science magazine fuels DNA testing controversy with prejudicial misquote
• Genetics & Public Policy Center – Marketing of unproven tests a threat to public health
• Wired – Lawless Gene-Testing Industry Needs a Sheriff, then updated with FDA, 23andMe Respond to Gene-Drug Test Article
• GenomeWeb Daily News – Policy Paper Calls for More Pharmacogenetic Oversight
• DNA Direct – DNA Direct Replies to Science: A Case Study of Personalized Medicine, and DNA Direct’s Official Response (pdf)
• Eye on DNA – Direct-To-Consumer Genetic Tests – Good or Evil?
• Ars Technica – Direct to consumer genetic testing raises concerns
• Bloomberg.com – Gene Tests May Be More Confusing Than Illuminating
• Personal Gene Scans – Personal gene scans: Vanity or science?

P.S. – another pet peeve is that the authors of these studies felt that public health is being threatened and wanted to educate the public, but submitted their article to a closed-access journal. A double-edged sword, I suppose; publish in a high-profile journal to attract attention, or risk less attention from publication in an open-access journal. This work was presumably funded by the Genetics and Public Policy Center, which in turn is funded by “The Pew Charitable Trusts, with research funding from the National Human Genome Research Institute and the U.S. Department of Veterans Affairs.” Thus it would appear that my tax dollars helped fund the work. I wish I could read it without paying $10 for access through Science.

At 12:01 on April 1, 2082, millions of genealogists around the solar system will be able to instantaneously download every image from the 2010 census into their neural storage chip, and within minutes these images will be linked to the ancestors in their 3D holographic family trees. Almost all of these genealogists will be able to find themselves in these census images and index.

Okay, maybe it’s a little premature to guess about the use of a census that hasn’t even been enumerated yet, but as most genealogists know, census results are the backbone of the genealogical world. Only one census has been released since the advent of the internet. In 2002 the 1930 census was released, and the countdown to the April 2, 2012 release of the 1940 census has already begun.

The 2010 census is only 2 years away. Here is the planned schedule for the 2010 census:

• March 2010 – Census questionnaires are mailed or delivered to households.
• April – June 2010 – Census workers visit households that did not mail back a census questionnaire.
• December 31, 2010 – U.S. population totals are due to the President.

On Thursday, it was announced that the government will not use handheld computers to collect information from Americans who fail to return their census forms (HT: GeneaSofts). Instead, census takers will use traditional pen and paper forms. It is estimated that this will increase the cost of the entire census to over $14 billion. That’s almost $47 per person!

Interestingly, however, the Census Bureau will still use GPS-enabled handheld computers to verify household locations in 2009, according to testimony from U.S. Secretary of Commerce Carlos M. Gutierrez on April 3rd. Wouldn’t it be great to have GPS coordinates associated with each census return?

Here is more information:

• CNN – Back to Pencil and Paper for 2010 Census, Fancy Computers Spell Trouble for 2010 Census.
• Salon.com – The 2010 Census Scraps Handhelds for Pen and Paper.
• Government Executive.com – On the Brink (a little sensationalist!!).
• And finally, the Statement of U.S. Secretary of Commerce Carlos M. Gutierrez Before the United States House Appropriations Subcommittee on Commerce, Justice and Science Thursday, April 3, 2008 (pdf).

Genealogy law lesson of the day:

Why are census records held for 72 years (other than the obvious public policy reasons)? Because of 36 C.F.R. §1256.4 (a)(3), which states the following:

“NARA will not grant access to restricted census and survey records of the Bureau of the Census less than 72 years old containing data identifying individuals enumerated in population censuses in accordance with 44 U.S.C. 2108(b).”

44 U.S.C. 2108(b) simply states that agreements between the Census Bureau and the National Archives, such as the 72-year agreement, become law. As to why it is 72 years and not 10 or 100 years, supposedly 72 was chosen because it was the average lifespan of Americans when the agreement was made.

Here is the abstract of today’s Y-chromosome haplogroup tree paper in Genome Research, I’m still working to get a copy of the actual paper (unfortunately, it’s not open access at this time):

Markers on the non-recombining portion of the human Y chromosome continue to have applications in many fields including evolutionary biology, forensics, medical genetics, and genealogical reconstruction. In 2002, the Y Chromosome Consortium published a single parsimony tree showing the relationships among 153 haplogroups based on 243 binary markers and devised a standardized nomenclature system to name lineages nested within this tree. Here we present an extensively revised Y chromosome tree containing 311 distinct haplogroups, including two new major haplogroups (S and T), and incorporating approximately 600 binary markers. We describe major changes in the topology of the parsimony tree and provide names for new and rearranged lineages within the tree following the rules presented by the Y Chromosome Consortium in 2002. Several changes in the tree topology have important implications for studies of human ancestry. We also present demography-independent age estimates for 11 of the major clades in the new Y chromosome tree.

Karafet, T.M., Mendez, F.L., Meilerman, M.B., Underhill, P.A., Zegura, S.L., and Hammer, M.F. New binary polymorphisms reshape and increase resolution of the human Y-chromosomal haplogroup tree. Genome Res. doi:10.1101/gr.7172008.

A long-anticipated new version of the Y-Chromosome Tree will be released in the journal Genome Research tomorrow (Wednesday, April 2nd). In the paper, scientists from the University of Arizona and Stanford University use recent SNP data and research to reformulate the familiar Y-chromosome tree (see, for example, the current tree at ISOGG). Here is the full text of the press release.  The paper should appear here as soon as it is made available by Genome Research tomorrow.

From the press release:

In an article published online today in Genome Research (www.genome.org), scientists have utilized recently described genetic variations on the part of the Y chromosome that does not undergo recombination to significantly update and refine the Y chromosome haplogroup tree. The print version of this work will appear in the May issue of Genome Research, accompanied by a special poster of the new tree.

Hammer’s group integrated more than 300 new markers into the tree, which allowed the resolution of many features that were not yet discernable, as well as the revision of previous arrangements.

Furthermore, Hammer explains that this work has resulted in the addition of two new major haplogroups, S and T, with novel insights into the ancestry of both. “Haplogroup T, the clade that Thomas Jefferson’s Y chromosome belongs to, has a Middle Eastern affinity, while haplogroup S is found in Indonesia and Oceania.”

Here is the full citation of tomorrow’s paper:

Karafet, T.M., Mendez, F.L., Meilerman, M.B., Underhill, P.A., Zegura, S.L., and Hammer, M.F. New binary polymorphisms reshape and increase resolution of the human Y-chromosomal haplogroup tree. Genome Res. doi:10.1101/gr.7172008.