January 2008 has been another interesting and busy month for genetic genealogy and personal genomics. Keeping track of the latest developments can be a challenge, so I thought I’d do a brief round-up of some of the headlines that I thought were particularly interesting. Happy reading!
- Hsien at Eye on DNA discusses the use of DNAWitness, a Bio-Geographical Ancestry analysis, to narrow the pool of potential suspects in a crime. This hotly debated test has been used in over 200 crimes. And am I the only one who thinks that DNAPrint Genomics needs to invest a little money to upgrade its web design? Hsien also highlights the genetic genealogy pages of Kevin Duerink, pages that I myself have found to be quite useful.
The DNA Network was full of news about 23andMe, Knome, and the newly-announced 1000 Genomes Project, which plans to sequence (can you guess?) 1,000 genomes from around the world. The 1GP will “receive major support from the Wellcome Trust Sanger Institute in Hinxton, England, the Beijing Genomics Institute (BGI) Shenzhen, China and the National Human Genome Research Institute (NHGRI), part of the U.S. National Institutes of Health (NIH).” Source.
Here’s a brief roundup of all the latest regarding the 1GP:
New information about 23andMe, including the launch of their new blog, the spittoon:
- Scienceroll, “Knome Begins Sequencing First Clients.” Remember that Knome is currently charging customers $350,000 to have their entire genome privately sequenced. As I recently commented at Eye on DNA, I think the price tag is too high in light of recent developments in technology. This is actually amazing, considering that $350,000 would have been a bargain in January 2007. Companies hoping to make money from sequencing are going to learn to act quickly and adapt even faster.
- SEQanswers.com, “deCODEme opens sample data set, check it out!“
And last but not least, are you worried about hair loss? A new company called HairDX offers a test that will examine SNP(s) on the X-chromosome, but the specifics are extremely vague at the moment, including a lack of information on their website. For more information, see My Biotech Life, “HairDX – the genetic test for hair loss” and Eye on DNA, “HairDX – Genetic Test for Male Pattern Baldness (be sure to read the comments to see information from Dr. Ann Turner).”
Here are few of the latest sources of information or discussion about 23andMe:
Mark Fletcher at Wingedpig.com writes about some “23andMe Updates.” Fletcher notes that Andrew Scheidecker has written a program that will extract and download your own raw SNP data from 23andMe (http://www.scheidecker.net/personal-genome-explorer/). Scheidecker writes that the program doesn’t violate 23andMe’s terms of service, but I recommend confirming that for yourself before you use this program. Fletcher also links to Kevin Kelly at the Quantified Self, who writes “23andMe, Alzheimer’s disease, and ApoE.” Kelly notes (as has Fletcher) that the rs1702 and rs4420638 SNPs tested by 23andMe are resulting in “no call” for many individuals. These two SNPs are believed to be associated with Alzheimer’s disease.
Remember, you heard it here first! The Houston Chronicle appears to have advance news that two companies, Family Tree DNA and Seqwright, are planning to launch products that will analyze DNA for genes associated with disease, similar to services offered by 23andMe and deCODEme. The news is casually mentioned in a news story published yesterday in that newspaper, and on one of the paper’s blogs.
In the first article, “Public Can Get Genes Tested“, there is a quote from Bennett Greenspan, president and chief executive of Family Tree DNA:
“[FTDNA is] betting that public demand will soar for health testing as well, despite the skepticism of some physicians. Greenspan said Family Tree will begin testing for specific disease genes in a month or two. ‘We’ve been peppered with requests from customers for this kind of service during the last 18 months,’ he said.”
A report published in the New England Journal of Medicine entitled “Letting the Genome Out of the Bottle – Will We Get Our Wish?” is getting a lot of coverage elsewhere, but I thought I’d add my two cents. The report’s authors are largely concerned with quality control, clinical validity (the actual predictive value of genetic tests), and utility (the balance of family history and genetic testing) of genome scans offered by companies such as 23andMe, deCODEme, and Navigenics. They also suggest that people wait for the science to catch up before purchasing genome scans. There is an NEJM audio interview with Muin Khoury, one of the authors of the study about the subject. Note that this particular report is about medical implications of genetic testing, not about genetic genealogy (two very different topics that were very confusingly jumbled in the recent article “A High-Tech Family Tree” from U.S. News & World Report).
Genizon BioSciences, a private firm in Quebec with about 135 employees, has been awarded $31 million from the Dutch venture capital firm Biotechnology Turnaround Fund to uncover associations between genes and diseases such as obesity, diabetes, and Alzheimer’s.
There are a number of companies concentrating on the correlation between genetics and disease, but the reason that Genizon BioSciences stood out to me is the source of the DNA that the company studies. Genizon uses DNA from descendants of the Quebec Founder Population. This population began with roughly 2,600 individuals who settled Quebec between 1608 and 1760 (although more than 15,000 French had immigrated to Quebec in this period, the vast majority continued to travel westward across Canada) and is estimated to be over 6 million people today. Genizon uses this unique population for a number of beneficial reasons, including:
Although the world of genetic genealogy has slowed from the furor of November and December 2007, there is still plenty of discussion and consideration going on around the blogosphere.
First, Ann Turner , co-author of “Trace Your Roots With DNA” and
moderator founder of the terrific Genealogy-DNA list has experimented with both deCODEme and 23andMe. Although she is still analyzing the results, she has a short write-up of deCODEme’s graphic presentations for comparing genomes (Word document here). The deCODEme comparison tool allows users to compare the degree of similarity between genomes, as long as the user has permission to compare. For those without a permissible genome to compare to, deCODEme provides reference samples from about 50 different populations. Ann points out that “it would be really interesting to hear if anybody is testing a number of close or distant relatives,” as their genome comparisons would be especially relevant.Â Update: A revised version of Ann’s document with comparisons to more individuals is available here (zip file).
Scientists from the University of Utah have traced a mutation in the adenomatous polyposis coli (APC) gene to a Mr. and Mrs. George Fry, who arrived in the New World aboard the William & Mary around 1630.
The mutation, c.426_427delAT, is believed to increase the carrier’s chances of developing colon cancer from 2 in 3 by age 80, a significant increase from the normal of 1 in 24. The study is available here for FREE – thank you open access – and is entitled “American Founder Mutation for Attenuated Familial Adenomatous Polyposis.”
Scientists traced two branches (from two of the Fry’s four children) of the family back to the Fry family, one in Upstate New York and one in Utah. The family in Utah, with more than 5,000 people, has been the focus of scientific study for over 14 years because of their unfortunately high risk of colon cancer. In fact, members of the Utah branch constitute 0.15% of all colon cancer in the state of Utah!
As of the end of November, the Personal Genome Project has a newly-designed and user-friendly website. Compare the OLD site and the NEW site – what an improvement! Misha Angrist, aka genomeboy.com and one of the “First 10″ aptly called the site “PGP 2.0″.
The new site is extremely well organized and contains information about the project and about participating in the project, if one is so inclined. Since this project will contain so much personal information about each individual that joins, participants will go through an extensive consent process that will include education, physician assistance, and even an online assessment to gauge the participant’s grasp of genetics and the risks of participation, among other things. I know that the team is working feverishly behind the scenes to gather as much information as possible to create an extensive consent protocol.
VortexDNA today announced the launch of myDNAchoice, a website and Firefox extension aimed at mapping the DNA of “human intention” to help users map their interactions with the internet. Nick Gerritsen, a director of VortexDNA, believes that “this includes better search results, meeting people like you, letting people find you on your favourite sites, and much more–without ever compromising your privacy.”
Although it is a bit confusing, myDNAchoice is a browser tool to help users organize the web based on their interactions with the internet, both previous (reflected in the short survey taken at installation) and future (new surveys taken through time). This browser tool, the company asserts, may result in as much as a 14% increase in search relevancy as compared to Google Search.A user begins by installing the mywebDNA Firefox extension in Firefox: