Misha Angrist wrote about the implications of personal genome sequencing in â€œWarts and all.â€
I think most everyone would agree that affordable whole-genome sequencing will be around long before we understand the information it reveals.I asked another member of The DNA Network, The Gene Sherpa his opinion on the matter.Genome Technology Online also thought it was an interesting discussion.And by the way, the Genome Technology Onlineâ€™s daily newsletter is a great way to stay up-to-date.
23andMe has been the subject of much discussion in the biotech and personalized medicine circles of the blogosphere (See here, here, here, here, here, here, here, and here for plenty of information/speculation/discussion).
In August, 23andMe announced (â€œ23andMe and Illumina Forge Consumer Genomics Goliathâ€) that they have partnered together to offer â€œconsumer genotypingâ€ – more about that in a minute.Illumina produces â€œSNP chipsâ€, chips that can test a genome for thousands of SNPs (single nucleotide polymorphisms) at a time.For example, the company has one chip that tests one million SNPs for as little as $600, and another chip that tests 550,000 SNPs (the HumanHap550) for only $300-$450.Interestingly, Illumina is also able to custom build chips to add specific SNPs if the customer so desires.Additionally, as the announcement touted, Illumina is also exploring the world of inexpensive whole-genome sequencing, suggesting that this partnership with 23andMe could transition from cheap SNP testing to cheap whole-genome sequencing at some point in the future.
If you’re interested, here’s a link to a document from the Edge Foundation, a group designed to promote the discussion of intellectual pursuits. The document is a summary (including video links) of a casual meeting between some fantastic scientific minds (Craig Venter, Freeman Dyson, Robert Shapiro, Dimitar Sasselov, and Seth Lloyd) which took place in late August.
Although Dr. Church doesn’t discuss the Personal Genome Project, his brief discussion about our past and our future is very interesting.Â There’s also a summary of the meeting from Gregory T. Huang, an invited journalist.Â I see that one of the invited guests was Ting Wu, a researcher at Harvard who has initiated the pgEd (personal genetics education project).
The DNA-NEWBIE mailing list is a great resource for people who are new to genetic genealogy or genetic testing in general. The list provides a forum for questions while promoting education and the sharing of ideas. I primarily use the mailing list to follow current trends or concerns in the field of genetic genealogy so that I can share them here on the blog.
The recent deluge of media attention regarding J. Craig Venter’s diploid genome sequencing prompted one list-member to quote Dr. Edward Rubin: “It’s not clear whether it’ll be 10 years or 50 years, but in our lifetime, [individual DNA sequencing ] will happen.” The list-member goes on to say that it will probably not happen in his lifetime since he turns 75 next month.
A very interesting article in the New Scientist published last week by Peter Aldhous examines the approach of affordable whole-genome sequencing. The article mentions 23andme, the recently published genomes of James Watson and J. Craig Venter, and the Personal Genome Project.
“Thanks to the advances in sequencing technology, that might be done for as little as $1000 per person. â€œDNA chipsâ€, meanwhile, can scan your genome for common â€œspelling mistakesâ€ for just a few hundred dollars. At that price, the era of personalised genomics is already dawning. â€œThis is the year,â€ claims [Dr. George] Church.”
Mr. Aldhous’ article doesn’t shy away from the hard stuff either. Although I could potentially obtain my entire genomic sequence if I had $1 million lying around, very little of the information would be interpretable. We still have so very much to learn about our DNA. A great quote comes from Michael Egholm of 454 Life Sciences:
A news release announces the completion of a DNA collection project by SMGF (Sorenson Molecular Genealogy Foundation) in Mongolia.The goal of the project is to study the descendants of ancient nomads from the Eurasian steppes.The collection was performed in conjunction with the National University of Mongolia and represents â€œthe most comprehensive [DNA collection project] in the history of Mongolia, incorporating all of the countryâ€™s geographic regions and major ethnic populations.â€In total, more than 3,000 DNA samples and pedigree charts were obtained from 24 different ethnic groups.
According to the news release, the â€œglobal fascination with Mongolian icons such as Genghis Khan and Attila the Hunâ€ played a role in promoting the project:
I recently had the opportunity to talk with Dana Waring, a member of Ting Wu‘s lab at Harvard and one of the creators/caretakers of the pgEd, the Personal Genetics Education Project. It was a fascinating conversation about the future of personal genetics and the dire need for more education of the public in this field. You can see a few recent mentions of the pgEd from other members of the DNA Network – EyeonDNA, and genomeboy.com.
I was very interested in Dana’s project, and she was willing to share more information with me and my readers via the following email interview:
TGG: How did you get involved with the Personal Genetics Education Project?
The Personal Genetics Education Project is based in the Wu lab at HarvardMedicalSchool. The main research focus of the lab is in a branch of epigenetics called homology effects, where the presence of homologous sequences can dramatically affect gene expression. Professor Wu wanted to add a new dimension to the labâ€™s focus, looking at the potential social impact of genetic testing becoming mainstream – personal genome sequencing to be exact.My background in womenâ€™s studies, the history of science, and higher education seemed like a good fit to explore some of the ethical, legal, and sociological ways genetics will personally impact people.With the Archon X Prize for Genomics and the Personal Genome Project well underway, it is clear that the science is moving very fast.
Wow, what a day for personal genetics. Yesterday, J. Craig Venter’s diploid genome was released (I’m not sure where the sequence is, but the paper is available at PLoS Biology, a OPEN ACCESS journal!).
I know that many people have their gripe about Venter, but seeing a story about personal genetics on the front page of CNN is important. It educates people and helps alleviate fears about genomic sequencing. I think it’s a great opportunity for the field. Here’s a few quotes from the CNN story:
“Venter has just published almost all 6 billion letters, or 96 percent, of his own personal genetic code in the journal PLoS Biology. From diseases to personality traits, it’s the most comprehensive human genome to date. Venter’s gene map provides a new understanding of his genetic destiny, according to the DNA inherited from both his father and his mother.
Itâ€™s always been my belief that personal genetics (inexpensive whole-genome analysis) will bring about some exciting changes in the field of genetic genealogy.One of the biggest areas of change will undoubtedly be in the area of autosomal genetic testing.(Remember that autosomal testing examines nuclear DNA, which is DNA other than mtDNA, Y-DNA, or X chromsomes).
A new study takes one of the first steps in the genetic genealogy revolution by examining SNP variations in four self-identified American populations â€“ European, Latino/Hispanic, Asian, and African American (see reference below).â€œThese population labels were used, despite the controversy surrounding the correspondence between notions of race and population structure inferred from explicit genetic data, because they are the labels used by NIH, FDA, and many, if not most, biomedical researchers.â€The researchers sequenced the exons and flanking regions of 3,873 genes from 76 unrelated individuals.