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.
As I mentioned back in June,Â Ancestry.com has teamed up with Sorenson Genomics to offer DNA testing.Â Today I received the following notification announcing the beta launch of dnaancestry.com.Â A Y-DNA test with 33 markers will be $149, while a Y-DNA test with 46 markers will be $199 (if you look at the sample results page, you’ll see a list of the 46 markers tested).Â An mtDNA test will be $179, although the exact testing parameters for the mtDNA test are unclear at this point (the website only states that HVR1 and HVR2 will be sequenced).
Introducing DNA Ancestry
We want you to be one of the first to know weâ€™re adding a powerful new dimension to genealogical research by integrating the worldâ€™s largest online collection of historical records and family trees with DNA testing. Currently in beta, DNA Ancestry is another way weâ€™re helping people expand their family trees and connect with family across distance and time.
Yesterday we saw that many funeral directors offer DNA retrieval and storage as one of their services.Today, weâ€™ll look into the WHY of DNA storage, and bring up some of the ethical questions it raises.
Why store DNA from the recently deceased?
Undoubtedly, someone who has never heard of DNA retrieval and storage will probably ask WHY we should store a dead relativeâ€™s DNA.
The reason most commonly quoted is that the DNA can be used in the future to identify inherited traits such as genetic disorders and other phenotypic characteristics.In 2006, the New England Historic Genealogical Society published an article by Edwin M. Knights, M.D. entitled â€œDNA Banking for Medical Information.â€In the article, Dr. Knights gives a number of reasons for banking DNA from both living and deceased individuals, many of which he gleaned from the Human Genetic Society of Australasia.He states:
The field of genomics is exploding.Every day, the mysteries of our genome are revealed and we learn more and more about the power of DNA.Soon, with affordable whole-genome sequencing, we will be able to analyze our own personal genome for clues about our ancestry, our propensity for disease, and insight into our body and our personality.In fact, this is already well underway.
Undoubtedly, each of us will be faced with a decision in our lifetime – do we want to learn the secrets of our genome, or do we want to live without that knowledge, as all of our ancestors have done for millions of years.This decision is a personal one, and at this point I donâ€™t think thereâ€™s any right or wrong answer.
But what about those who are unable to make that decision?For example, an infant is unable to give consent for genetic testing, but many states in the USroutinely test newborns for genetic disorders.Today and tomorrow we will be examining another group of individuals who are not able to consent to genetic testing â€“ the recently deceased.
A study in the September Journal of Field Archaeology analyzes mtDNA that was isolated from Native American aprons and from quids – chewed plant material.Â From an article in science:
“The quids and aprons belonged to a vanished tribe that archaeologists call the Western Basketmakers. Between about 500 B.C.E. and 500 C.E., they lived in caves and rock shelters in what is now southern Utah and northern Arizona.”
“They pulled mitochondrial DNA from 48 quids and from 18 aprons that had been stained with what was likely menstrual blood. Then they scanned the DNA for various molecular markers called haplogroups, which appear in different frequencies in different parts of the world.”
The researchers discovered that 14% of the samples belonged to Haplogroup A.Â They also point out that museum and university collections have many sources of Native American DNA (such as quids, textiles, and cigarettes).