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Pathway Genomics Goes Live

imageThe newest entrant in the field of personal genomics has officially gone live.  Pathway Genomics, located in California, uses SNP testing to examine information about Health conditions, Ancestry, Carrier Status, Personal Traits, and Drug Response.  The company collects DNA via a spit kit, and has its own lab on-site:

We decided early on that the surest way to completely secure your information would be to build our own CLIA-certified laboratory. And that’s just what we did. Once we receive your saliva sample in our lab, your DNA never leaves the building. As a matter of fact, we place it in our proprietary DNA Lockbox for safekeeping. No other DNA testing firm offers this level of security. Others send your DNA elsewhere for testing, even to non-secure overseas locations!

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Genome Hacking at The New Scientist

Journalists Peter Aldhous and Michael Reilly write about using DNA obtained from a drinking glass and other sources to “hack” someone’s genome.

In “Special investigation: How my genome was hacked,” the authors use a variety of consumer-available DNA services to prepare and amplify genomic DNA in order to send it away for analysis by deCODEme.  They used deCODEme, it appears, because 23andMe and Navigenics use saliva collection, and “it would be hard to convert [the] amplified DNA sample into a form that closely mimicked saliva.”  They did use 23andMe, however, as a control.  Interestingly, the cost of the entire process was about $1,700 for lab services (preparation and amplification) and $985 for deCODEme’s service.

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The Close Cousins DNA Project – A Request for Help

Chimpanzee

Image by Aaron Logan

Roughly 6 million years ago, the Hominini subtribe of the Hominidae family tree (the so-called “great apes”) diverged into two known branches, with one branch (genus Pan ) resulting in modern-day Chimpanzees and Bonobos, and the other branch (genus Homo) resulting in modern-day humans.

Since there has only been 6 million years of divergent evolution, Chimpanzees/Bonobos and Humans share a great deal of DNA sequence in common (although estimates vary widely and typically depend on what, exactly, is being considered in the comparison).

The Close Cousins DNA Project

On May 31, 2008, the Close Cousins DNA Project was launched by Bill Davenport as a result of a discussion on the Genealogy-DNA mailing list regarding the relatedness of human and chimpanzee Y-DNA.  From the launching post:

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5th International Conference on Genetic Genealogy for Family Tree DNA Group Administrators

On March 14th and 15th of this year, Family Tree DNA hosted the 5th Annual Conference on Genetic Genealogy.  From the press release (pdf):

Each year, world renowned experts in genetics and science present cutting-edge developments and exciting new applications at this two-day educational forum which draws attendees from Family Tree DNA’s Group Administrators in North America and throughout the world. Among the speakers at the upcoming conference will be Dr. Spencer Wells, the director and population geneticist heading the National Geographic’s landmark Genographic Project as well as members of Family Tree DNA’s own highly respected scientific advisory board.

The schedule of the conference can be found here.  Unfortunately, I was not able to attend the conference this year, although I certainly hope to attend the next conference. 

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Visualizing Your Genetic Genealogy

In my genealogical research, I have sometimes found myself missing the trees by focusing on the forest.  I think it happens to many genealogists – we get caught up in the research, the dates, the places, and we forget that there was so much more to people than their vital statistics.

This can happen to genetic genealogists as well.  The connection between the results of a DNA test and the individuals in our tree can be easy to forget and difficult to visualize.  Take the results of an mtDNA test, for example.  The results are obtained from a tiny piece of DNA that has traveled thousands of years (and often thousands of miles) through hundreds of individuals to end up in your cheek cells and on the tip of a swab.  Everyone’s mtDNA is the product of an amazingly rich story that has largely been lost to history.

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Genetic Testing With 23andMe – Ancestry Testing

Yesterday I posted about my recent testing experience with 23andMe, focusing on the health and traits information.  This post examines the genealogical aspects of testing at 23andMe.

Ancestry Information

Although I was interested in the health and traits information, I was most excited about the ancestral information.  23andMe’s test looks at mtDNA, Y-DNA, and autosomal coverage.  I believe that the company is working to report on ancestry of the X-chromosome, but as I have previously reported X-DNA ancestry can be extremely challenging.

This was my second foray into autosomal DNA testing.  In 2003 I purchased an AncestrybyDNA 2.0 test from DNAPrint Genomics.  The test looked at 71 Ancestry Informative Markers (AIMs) to determine percentages of Indo-European, East-Asian, Native-American, and African ancestry.  It is worth noting that before AncestrybyDNA went out of business (more info here), the company was offering more advanced tests that examined as many as 1,700 markers (still far below the number of markers used to quantify percentages at 23andMe and deCODEme).

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Genetic Testing With 23andMe

This is the first entry in a two-part series describing my recent experiences with genetic testing through 23andMe.  Although I was most excited by the genetic genealogy information provided by the results, I thought that readers might be interested in some of the health and trait information as well.  If I forget to discuss something, feel free to ask in the comments and I’ll do my best to respond.

Note that this discussion is limited to a cursory analysis of my results.  Anyone who is considering testing through 23andMe should be aware that scientists are only just beginning to study and understand the connection between genetics and health, and thus the results are not meant to be interpreted as absolutes.  Be sure to analyze your own results with this caveat in mind, and do your own research into the testing process.

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GeneTree Announces Web Site Out Of Beta

image In October 2007, I wrote about the launch of GeneTree (see “Sorenson Genomic’s GeneTree Launches”), a “DNA-enabled family history-sharing Web site.”  Today, GeneTree has announced that it is out of beta and has added advanced features for users.

Press Release

Following is the press release from GeneTree:

SALT LAKE CITY (March 9, 2009)—GeneTree today announced its free family Web site has completed beta testing and now offers those who sign in a simple, intuitive way to regularly communicate with their extended family and to securely share and store family contact information, personal profiles, photos, video and ancestry documents. Advanced features now available through GeneTree’s redesigned graphic interface include GEDCOM file-format import for family tree collaboration, paternal line genetic genealogy and an all-new family tree building tool.

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Interviews with 23andMe Customers

Image representing 23andMe as depicted in Crun...

Image via CrunchBase

DAVIDE at the European Genetics and Anthropology Blog recently posted two interviews (here and here) with customers of 23andMe’s large-scale genome scanning service, one from Finland and one from the U.S.

It’s very interesting to see the responses of these anonymous individuals, particularly since they are from different countries.

For example, both were asked why they decided to purchase the 23andMe test – “Was it to test your ancestry or genetic health risk factors?”  Interestingly, for both individuals ancestry was the motivating factor behind testing.  More support for my conclusion that these companies should strongly promote the ancestral aspects of their products.

Other Questions

Here are a few examples of other questions in the interviews:

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DNAPrint Genomics Ceases Operations

dnaprintgIn February, I received a number of comments and emails which suggested that DNAPrint Genomics was not processing results and could not be reached by telephone.  DNAPrint was one of the first companies to offer ‘large-scale’ autosomal testing, although their tests were unable to compete with the testing currently offered by companies like 23andMe and deCODEme.

Indeed, the company has recently ceased operations.  From the site: “DNAPrint® Genomics, Inc. has regrettably ceased operations. We thank you for your support.”  As I wrote last February, the company was scheduled to be purchased by Nanobac Pharmaceuticals, but the deal fell through shortly thereafter.

GenomeWeb Announces DNAPrint’s Demise

From an announcement today at GenomeWeb – “DNAPrint Genomics Goes Bust”:

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