The Genetic Genealogist

Genome Technology Online mentioned the new partnership between DNAPrint Genomics, Inc. and BioServe, a company that offers “the Global Repository®, a growing library of over 600,000 human DNA, tissue and serum samples linked to detailed clinical and demographic data from 140,000 consented and anonymized patients from four continents.”

As part of the partnership, DNAPrint will analyze the 600,000 human samples in the Global Repository using the ANCESTRYbyDNA test. According to Richard Gabriel, the CEO and President of DNAPrint Genomics:

“By removing the question of ancestry from a clinical sample researchers can more readily evaluate which medicines will produce side effects within certain ethnic groups, and which medicines will work for the widest spectrum of a population.”

The CEO of BioServe, Dr. Kevin Krenitsky, stated in the press release that “now that we are able to add the genetic ancestry component to our samples, a new layer of sample data quality and analysis can be provided that was not previously available to researchers.”

An order of 600,000 ANCESTRYbyDNA tests will be quite a boon for DNAPrint Genomics, which has been actively seeking markets other than traditional genetic genealogy consumers. And it is possible that this initiative will create a demand for this type of data in many more studies of biological samples.

I’ve spoken before about the enormous effect that affordable SNP and whole-genome sequencing will have on genetic genealogy. In that previous article, I mentioned a study using SNP analysis to identify a person’s ancestry based on autosomal DNA (all the nuclear non-sex DNA). Another study, released today in PLoS Genetics, used SNP chips to identify SNP markers that are characteristic of a certain ancestral origins. According to the authors:

“We have developed a novel algorithm to identify a subset of SNP markers that capture major axes of genetic variation in a genotypic dataset without use of any prior information about individual ancestry or membership in a population.”

To accomplish this, the researchers:

“…studied here 274 individuals from 12 populations (20 Mbuti, 20 Mende, 22 Burunge, 42 African Americans, 42 Caucasians, 20 Spanish, 11 Mala, 20 East Asians, 20 South Altaians, 20 Nahua, 20 Quechua, and 19 Puerto Ricans). Three of these populations are admixed (Caucasians, African Americans, and Puerto Ricans). All individuals were typed using the 10K Affymetrix array.”

The “10K Affymetrix array” is a chip that tests for about 11,500 SNPs (single nucleotide polymorphisms, or mutations) in each individual. Personally, I don’t know why more genetic genealogy companies aren’t doing this type of research themselves. The chips are relatively cheap these days, and there are plenty of people willing to send in DNA from all around the world with extensive ancestral information. This is the future of genetic genealogy, and they should be a part of it.

The most interesting paragraph from the news release:

“Their program was more than 99 percent accurate and correctly identified the ancestry of hundreds of individuals. This included people from genetically similar populations (such as Chinese and Japanese) and complex genetic populations like Puerto Ricans who can come from a variety of backgrounds including Native American, European, and African.”

The researchers then used their data to analyze an admixed population to evaluate their results, with great success. Here’s a figure related to the paper, here is Dr. Petros Drineas‘ lab website, and here’s the entire news release:

“A group of computer scientists, mathematicians, and biologists from around the world have developed a computer algorithm that can help trace the genetic ancestry of thousands of individuals in minutes, without any prior knowledge of their background. The team’s findings will be published in the September 2007 edition of the journal PLoS Genetics.

Unlike previous computer programs of its kind that require prior knowledge of an individual’s ancestry and background, this new algorithm looks for specific DNA markers known as single nucleotide polymorphisms, or SNPs (pronounced snips), and needs nothing more than a DNA sample in the form of a simple cheek swab. The researchers used genetic data from previous studies to perform and confirm their research, including the new HapMap database, which is working to uncover and map variations in the human genome.

“Now that we have found that the program works well, we hope to implement it on a much larger scale, using hundreds of thousands of SNPs and thousands of individuals,” said Petros Drineas, the senior author of the study and assistant professor of computer science at Rensselaer Polytechnic Institute. “The program will be a valuable tool for understanding our genetic ancestry and targeting drugs and other medical treatments because it might be possible that these can affect people of different ancestry in very different ways.”

Understanding our unique genetic makeup is a crucial step to unraveling the genetic basis for complex diseases, according to the paper. Although the human genome is 99 percent the same from human to human, it is that 1 percent that can have a major impact on our response to diseases, viruses, medications, and toxins. If researchers can uncover the minute genetic details that set each of us apart, biomedical research and treatments can be better customized for each individual, Drineas said.

This program will help people understand their unique backgrounds and aid historians and anthropologists in their study of where different populations originated and how humans became such a hugely diverse, global society.

Their program was more than 99 percent accurate and correctly identified the ancestry of hundreds of individuals. This included people from genetically similar populations (such as Chinese and Japanese) and complex genetic populations like Puerto Ricans who can come from a variety of backgrounds including Native American, European, and African.

“When we compared our findings to the existing datasets, only one individual was incorrectly identified and his background was almost equally close between Chinese and Japanese,” Drineas said.

In addition to Drineas, the algorithm was developed by scientists from California, Puerto Rico, and Greece. The researchers involved include lead author Peristera Paschou from the Democritus University of Thrace in Greece; Elad Ziv, Esteban G. Burchard, and Shweta Choudhry from the University of California, San Francisco; William Rodriguez-Cintron from the University of Puerto Rico School of Medicine in San Juan; and Michael W. Mahoney from Yahoo! Research in California.

Drineas’ research was funded by his National Science Foundation CAREER award.”

There’s still a long way to go, but this is a great start.

Non-Scientist Summary: A group of researchers used SNP (single nucleotide polymorphism) analysis to identify particular SNPs which are associated with an individual’s particular ancestry (for example, Caucasian, African American, Japanese, etc..). Using this information, they could test individuals with unknown ancestry for those SNPs, in effect characterizing their ancestry based on the SNPs that they possess.

It’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 – European, Latino/Hispanic, Asian, and African American (see reference below). “These 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.” The researchers sequenced the exons and flanking regions of 3,873 genes from 76 unrelated individuals.

Results:

SNPs common in one population were frequently not common in other populations. “Moreover, SNPs that were common in two or more populations often differed significantly in frequency from one another, particularly in comparisons of African Americans versus other U.S. populations. These findings indicate that even if the bulk of alleles underlying complex health-related traits are common SNPs, geographic ancestry might well be an important predictor of whether a person carries a risk allele. “

“A frequent claim about human population structure is that most common variation is shared among all populations. This, of course, depends on how population boundaries are defined, but often cited to support such comments are the comparisons of SNP frequencies in pairs of populations in the HapMap data and the Perlegen data. Analyses of these data indicated that common SNPs were frequently both shared and common among populations of predominately African, Asian, and European ancestry. However, population genetic analysis was not the intended goal of either the HapMap or the Perlegen projects, and common, shared SNPs were over sampled by the ascertainment strategies used for each project.”

The structure of common SNP variation differed substantially in African Americans compared with all other U.S. populations studied. “The largest absolute number of SNPs, common SNPs, and private SNPs were found in African Americans. African Americans exhibited the highest proportion of rare SNPs (64%), the lowest proportion of common SNPs (36%), and nearly half of all SNPs (44%) in African Americans were private.”

Although I still think it is too early for useful autosomal testing, this type of data suggests that there is a bright future for geographic ancestry.

Reference: The Structure of Common Genetic Variation in U.S. Populations. Stephen L. Guthery, Benjamin A. Salisbury, Manish S. Pungliya, J. Claiborne Stephens, and Michael Bamshad. The American Society of Human Genetics (Link(pdf, requires subscription)).

HT: Dienekes’ Anthropology Blog

A study in the September Journal of Field Archaeology analyzes mtDNA that was isolated from Native American aprons and from quids – chewed plant material.  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.  They also point out that museum and university collections have many sources of Native American DNA (such as quids, textiles, and cigarettes).

Yesterday I wrote about a study that used SNPs to haplotype the Y chromosomes of ancient DNA obtained from skeletons found along the Yangtze River in China. The ability to extract and use SNP data from ancient Y-DNA is a relatively new scientific development. Indeed, the author’s of the study I highlighted yesterday stated: “The first reported ancient Y SNP data was typed from a Native American sample of an extinct tribe (Kuch et al. 2007).” I thought I’d briefly mention this earlier study as well since it contains a lot of interesting information.

The Beothuk were a Native American group that lived on Newfoundland at the time of John Cabot’s arrival in 1497. Although estimates vary widely, they may have been as few as 500 to 1000 individuals. The Beothuk avoided Europeans, and eventually disease and conflict led to their extinction in the 1820s.

Researchers set out to investigate the origin and diet of the Beothuk by examining the DNA of two Beothuk individuals, Demasduit and Nonosabusut. Their skulls, dated between 1819 and 1820, are housed in the National Museums of Scotland in Edinburgh. One tooth from each skull was removed and used for the analysis.

The female’s mtDNA contained mutations 16223, 16298, 16325, and 16327 (Haplogroup C), while the male’s mtDNa contained mutations 16093, 16189, 16213, 16223, and 16278 (Haplogroup X). To confirm the haplogroup designation of the female as C, the researchers cloned the area containing the HincII site at 13,259 and discovered that it contained the A-G substitution characteristic of Haplogroup C. They also identified the SNP at position 16213 in the male sample which denotes Haplogroup X2a. And finally, the researchers sequenced a portion of the Y chromosome and identified the C to T substitution that is characteristic of the Native American Q-M3 lineage. These results “do not lend credence to the proposed idea that the Beothuk (specifically, Nonosabasut) were of admixed (European-Native American) descent.”

Analysis of dentine collagen and tooth enamel stable-isotope rations suggested that a significant portion of the Beothuk’s diet consisted of marine foods, and that they drake mostly lake water rather than river water.

Isn’t it amazing what a single tooth can reveal?

Citation:

Kuch M, Grocke DR, Knyf MC, Gilbert MT, Younghusband B, Young T, Marshall I, Willerslev E, Stoneking M, Poinar H (2007) A preliminary analysis of the DNA and diet of the extinct Beothuk: a systematic approach to ancient human DNA. Am J Phys Anthropol 132(4):594–604.

In the past, scientists have primarily examined the mtDNA of ancient DNA. After all, mtDNA is much more prevalent (100’s to 1000’s of copies per cell) than nuclear DNA (just 1 copy per cell) and thus it is easier to find samples that are not degraded by time. New amplification techniques as well as improved anti-contamination procedures have made it possible for Y chromosomal DNA to be

In a new study (epub ahead of print – which means that it is available online before it is published in Human Genetics), researchers examined the remains of male skeletons that were buried in the loessal soil in Maqiao, Xindili, Wucheng, Daxi, and Taosi, areas along the Yangtze River. Interestingly, these skeletons were buried without chests or coffins. Using a well-established set of anti-contamination procedures, DNA was extracted and five SNPs were typed for each individual (when possible): M119, M95, M122, M7, and M134. According to YCC nomenclature, those SNPs delineate the O1, O2a, O3*, O3d, and O3e haplogroups. The scientists found that:

“[A]t least 62.5% of the individual remains (30 out of 48) belong to O haplogroup, which is still the major haplogroup of today’s East Asians. These ancient results, consequently, did not differ from the modern populations. The resulting DNA types thus made “phylogenetic sense” (the Y chromosome haplogroup structure), helping to verify the authenticity of the ancient DNA.”

Citation:

Li H, Huang Y, Mustavich LF, Zhang F, Tan JZ, Wang LE, Qian J, Gao MH, Jin L. (2007) Y chromosomes of prehistoric people along the Yangtze River. Hum Genet. 2007 Jul 27; [Epub ahead of print].

HT: Dienkes’ Anthropology blog.

A recent study (epub ahead of print) published in Human Heredity examines the Y-DNA and mtDNA haplogroups of 120 black males from Sao Paulo, Brazil. Approximately four million Africans were taken as slaves to Brazil where they interbred extensively with Amerindians and Europeans. Previous studies from this group have shown that while white Brazilians have predominately European Y-DNA, they have high a proportion of African and Amerindian mtDNA.

Interestingly, the study showed that while only 48% of the Y-DNA was characteristic of sub-Saharan Africa, 85% of the mtDNA appeared to be of African origin. The authors also used the results to estimate the ancestral contribution of Central-West, West, and Southeast Africa to African Brazilians from Sao Paulo. I can’t reveal those time estimates, however, because I don’t have access to the article.

The supplemental data is free, including a supplementary table (pdf) of the HVS-I (16065-16365) sequence variations from each of the 120 individuals.

HT: Dienekes’ Anthropology Blog

Here they are, the “First 10″, the first ten volunteers of the Personal Genome Project, announced today:

• Misha Angrist, Ph.D. is Senior Science Editor at the Duke Institute for Genome Sciences and Policy in Durham, N.C. His work has appeared in The Michigan Quarterly Review and the Best New American Voices anthology, among other places. Dr. Angrist is also an independent consultant to the life sciences industry. He earned his M.S. in biology from the University of Cincinnati and his Ph.D. in genetics from Case Western Reserve University. His doctoral work focused on the complex inheritance of Hirschsprung disease. Following completion of his post-doctoral in 1998, Dr. Angrist covered the life sciences industry as an analyst for The Freedonia Group and was portfolio manager for the hedge fund Biotech Horizons Fund, LP. Dr. Angrist also holds a M.F.A. from the Bennington Writing Seminars. His firm, Ars Vita Consulting, Inc., provides insight to clients in the biotechnology, pharmaceutical, and broader healthcare arenas. For recent news by or about Dr. Angrist, see The New Atlantis and Future Medicine.

• Keith Batchelder, M.D. is the founder and CEO of Genomic Healthcare Strategies. Dr. Batchelder received an MD from Hahnemann University School of Medicine, an MS in Materials Science from New York University, a DMD from the University of Connecticut School of Dental Medicine, and a BA in physics from Middlebury College. Dr. Batchelder has been a consultant for personalized health and wellness companies such as Lineagen and an officer in several health-care organizations. He was chief technical officer of Worldcare Clinical Trials, and was a core member of the team that created Harvard Salud Integral, a new HMO in Mexico City, where he helped secure angel funding in a newly privatized healthcare environment and helped to grow the plan to cover 150,000 patients. He was also an early principal with Amicas, a company that was successfully sold for approximately $30 million cash and stock equivalents. For recent news about Dr. Batchelder, see Nature, Mass High Tech, and an interview with our own EyeonDNA!

• George M. Church, Ph.D. is a Professor of Genetics at Harvard Medical School and Professor of Health Sciences & Technology at Harvard and MIT. With Walter Gilbert he developed the first direct genomic sequencing method in 1984 and helped initiate the Human Genome Project in 1984 while he was a Research Scientist at newly-formed Biogen Inc. He invented the broadly-applied concepts of molecular multiplexing and tags, homologous recombination methods, and DNA array synthesizers. Technology transfer of automated sequencing & software to Genome Therapeutics Corp. resulted in the first commercial genome sequence, (the human pathogen, Helicobacter pylori) in 1994. He initiated the Personal Genome Project (PGP) in 2005 and research on synthetic biology. He is director of the U.S. Department of Energy Center on Bioenergy at Harvard & MIT and director of the National Institutes of Health (NHGRI) Center of Excellence in Genomic Science at Harvard, MIT & Washington University. He has been advisor to 22 companies, most recently co-founding (with Joseph Jacobson, Jay Keasling, and Drew Endy) Codon Devices, a biotech startup dedicated to synthetic biology and (with Chris Somerville) founding LS9, which is focused on biofuels. He is a senior editor for Nature EMBO Molecular Systems Biology. See the Boston Globe, Technology Review, his departmental page, his lab webpage, and our very own PersonalGenome.

• Esther Dyson is an active member of a number of non-profit and advisory organizations. From 1998 to 2000, she was the founding chairman of ICANN, the Internet Corporation for Assigned Names and Numbers. She has followed closely the post-Soviet transition of Eastern Europe, and is a member of the Bulgarian President’s IT Advisory Council, along with Vint Cerf, George Sadowsky, and Veni Markovski, among others. She has served as a trustee of, and helped fund, emerging organizations such as Glasses for Humanity, Bridges.org, the National Endowment for Democracy, and the Eurasia Foundation. She is also a member of the board for The Long Now Foundation, trustee for the Santa Fe Institute, the Advisory Board of the Stockholm Challenge Award and is a part-owner of the First Monday journal. She is a member of the President’s Export Council Subcommittee on Encryption and sits on the boards of the Electronic Frontier Foundation, Scala Business Solutions, Poland Online, Cygnus Solution, E-Pub Services, Trustworks (Amsterdam), IBS (Moscow), iCat, New World Publishing and the Global Business Network. She is on the advisory boards of Perot Systems and the Internet Capital Group, and a limited partner of the Mayfield Software Fund. She has also been a board member or early investor in tech startups, among them Flickr, PowerSet.com, ZEDO, Medscape, Medstory, XCOR, Constellation Services, Zero-G,Icon Aircraft and Space Adventures. Ms. Dyson is the daughter of Freeman Dyson, a physicist, and Verana Huber-Dyson, a mathematician. She holds a Bachelor’s degree in economics from Harvard University (1972). For recent news about Ms. Dyson, see The Huffington Post, Media Visions, MediaPost, and The Wall Street Journal.

• Rosalynn Gill-Garrison, Ph.D., is a founder and Chief Science Officer of Sciona, an international company that provides personalized health and nutrition recommendations based on an individual’s diet, lifestyle and unique genetic profile. Dr. Gill-Garrison is also on the panel of experts at Genelex. Dr. Gill-Garrison received her Ph.D. in Biological Sciences at the University of Texas at Austin, where she focused on the DNA-damaging effects of polycyclic aromatic hydrocarbons in animal and bacterial models. She went to the UK in1994 to the Department of Oncology at University College London before co-founding Sciona in 2000. For recent news about Dr. Gill-Garrison, see Time, MedScape, The Scientist, and the BBC.

• John D. Halamka, M.D., M.S., is Chief Information Officer of Harvard Medical School, Chief Information Officer of Beth Israel Deaconess Medical Center, Chairman of the New England Health Electronic Data Interchange Network (NEHEN), Chief Information Officer of the Harvard Clinical Research Institute (HCRI), and an Associate Professor of Emergency Medicine at Harvard Medical School. Dr. Halamka completed his undergraduate studies at Stanford University where he received a degree in Medical Microbiology and a degree in Public Policy with a focus on technology issues. Dr. Halamka received a medical degree at the University of California San Francisco while pursuing graduate work in Bioengineering at the University of California, Berkeley, focusing on technology issues in medicine. For recent news about Dr. Halamka, see The Boston Globe, BIDMC News, Yahoo Finance News, a podcast about health information exchange, and a newscast about online medical records.

• Stanley N. Lapidus, B.S.E.E., is the President and CEO of Helicos, a company that develops genetic analysis technologies for research, drug discovery, and clinical diagnostics markets. Helicos is Mr. Lapidus’ third life-science startup. In 1995 he founded EXACT Sciences Corporation, an applied genomics company that develops and markets non-invasive, DNA-based methods for early detection of colorectal and other common cancers. He served as the CEO from 1995 to 2001 and Chairman of EXACT Sciences’ Board of Directors from 2000 until the end of 2005. Prior to EXACT, Mr. Lapidus founded Cytyc Corporation and was President and CEO from 1987 through 1994. In addition to his entrepreneurial activities, Mr. Lapidus holds academic appointments in the Pathology Department at Tufts University Medical School and MIT’s Sloan School of Management. He earned a BSEE from Cooper Union. He has served as a trustee of Cooper Union since 2002. Mr. Lapidus holds 30 issued patents. For recent news about Mr. Lapidus, see Flagship Ventures, MarketingVP, The Hazelton Group, and Technology Review.

• Kirk M. Maxey, M.D. is the President of Cayman Chemical, a research biochemical company he started while still a student. After receiving his B.S. in Chemistry from Colorado State University, Dr. Maxey worked as a chemist at the Upjohn Company in Kalamazoo, Michigan. He later received his M.D. from the University of Michigan. Dr. Maxey has been a consultant and expert witness for Alcon and Pfizer as well as a contributing editor and reviewer for Prostaglandins and Other Lipid Mediators. While a student in the 1980′s, Dr. Maxey was a frequent contributor at sperm banks. contributed For recent news about Dr. Maxey, see PBS and ABC News.

• James L. Sherley, M.D., Ph.D. was formerly an associate professor in the Biological Engineering Division at the Center for Environmental Health Sciences in the Massachusetts Institute of Technology. He earned an M.D. and a Ph.D. in molecular biology from the Johns Hopkins University School of Medicine in 1988. Dr. Sherley’s laboratory addressed the problems that limit the development of adult stem cells for biomedicine. Dr. Sherley’s awards include the 2006 NIH Director’s Pioneer Award, an award from the Pew Scholars Program in the Biomedical Sciences, selection for the Pew Science and Society Institute, and the Ellison Medical Foundation Senior Scholar Award in Aging. For recent news about Dr. Sherley, see Future Health, Boston.com, Diverse Education, The Chronicle, and Boston.com.

The 10th participant has not yet given permission for the release of his/her name. From the announcement:

“Word in the newsroom is that InSequence will have a full feature story, with interviews of the participants, in tomorrow’s edition of the newsletter. If you’re a subscriber, you’ll be able to access it here.”

There’s a great recent article in Scientific American entitled “What Finnish Grandmothers Reveal about Human Evolution” highlighting the research of biologist Virpi Lummaa. I’ve mentioned before that while genetics is a useful tool for genealogical research, genealogy can also be a useful tool for genetic research! Dr. Lummaa’s research does exactly that.

Dr. Lummaa used 200 years of genealogical records to study the influence of evolution on reproduction”

“The 33-year-old Finnish biologist, aided by genealogists, has pored through centuries-old tomes (and microfiche) for birth, marriage and death records, which ended up providing glimpses of evolution at work in humanity’s recent ancestors.”

Dr. Lummaa proposes the following findings from her research of pre-modern Finns

• Male twins affect the mating potential of their female twins – the females are 25% less likely to have children and were 15% less likely to marry than female twins born with a sister. (Don’t worry, the article discusses many of the other variables that the study addressed). This finding is odd, because it suggests that there should be selection AGAINST opposite-sex twinning.

• Mothers who gave birth to sons had shorter life spans than those who gave birth to daughters. Dr. Lummaa proposes that this is due to larger birth weight, the testosterone that crosses the placenta, and the fact that boys tend to leave the nest while girls tend to stay close.

• Grandmothers are important to the survival of grandchildren. The presence of a grandmother might improve the reproductive potential of her grandchildren. This could, in part, explain why humans live so long after the end of their reproductive stage.

• Here’s another controversial finding – child mortality was higher in mainland towns than on the islands of Finland’s Archipelago Sea, presumably because mainland women replaced mother’s milk with cow’s milk much earlier.

It’s important to keep in mind, of course, that this research was carried out by studying the records of pre-modern people. Additionally, there are numerous cultural and social aspects that might influence the results, although Dr. Lummaa addresses some of them in the article.

(I just received a Google alert about this article – I’m not sure why it took so long for the article to be indexed. By the way, if you’re interested in the latest news about a certain topic, I highly recommend setting up a Google Alert. I don’t think a blogger could survive without it!).

Esther Dyson is a prominent force in the digital world, and is considered to be a member of the ‘digerati’ (a term for people who are the movers and shakers of everything technological). She is the daughter of the famous physicist Freeman Dyson and the mathematician Verana Huber-Dyson.

According to Wikipedia, the company that Ms. Dyson founded, EDventure Holdings, analyzes the impact of emerging technologies and markets on economies and societies. In addition, Ms. Dyson is on the board of the genetics company 23andme. Her interest in genetics and emerging technology is undoubtedly one of the main reasons she has decided to become one of the “First 10.”

The “First 10”

The “First 10” (or “First Ten”) references ten volunteers who are part of the Personal Genome Project, or the PGP. The PGP, headed by Dr. George M. Church of Harvard, aims to develop affordable personal genome sequences as well as user-friendly data applications. Initially, the project will start by releasing the sequencing and complete medical records of 10 individuals. Because of issues of risk versus benefit and informed consent, the first set of ten volunteers will be people who have a “master’s level or equivalent training in genetics or equivalent understanding of genetics research.” According to the PGP website, “[p]roduction costs per subject range from $8K for a limited subset of the genome to over $200K per subject to cover a significant fraction of their DNA.” According to a recent New York Times article, the “project’s volunteers will receive the one percent of their genome currently deemed most useful at a cost of $1,000.” This conflicts with the PGP’s description of the cost, and I’m not sure what the discrepancy is about.

Ms. Dyson’s Decision to Become One of the “First 10”

Ms. Dyson recently gave a short talk (the video is available here) at Fortune’s iMeme conference in San Francisco about her part in the Personal Genome Project. A summer of the talk was posted at Xconomy.com, “Learning from Esther Dyson’s Genome”:

“Famous venture capitalist Esther Dyson explained her reasons for being one of Church’s first ten volunteers last week at Fortune’s first iMeme conference in San Francisco. Church (who is also an Xconomist) hopes to gather enough data from the project to speed research into the links between gene variations and both common and rare human diseases, and to accelerate progress toward more individualized health care based on patients’ genetic profiles.”

In the comment section of the Xconomy.com post, you’ll find a thought-provoking conversation led by Willy Lensch, Ph.D. ThePersonalGenome.com pointed out that the Dr. Lensch’s first comment ended with a great sentence, so go check it out.

“Full Disclosure”

This week also saw an entire article in the Wall Street Journal titled “Full Disclosure” by Ms. Dyson. In the article, Ms. Dyson points out that sometime this summer or early fall, her genome, her answers to a substantial health questionnaire, and all her medical records will be posted on the Internet for the entire world to see:

“I’m one of 10 members of Harvard geneticist George Church’s Personal Genome project. We all come to this with slightly different motivations, histories and medical records. But we share, in theory, the equivalent of a master’s degree in genetics, an age between 30 and 100, and a willingness to come to Boston to give blood, get our faces professionally photographed and sit down with one another to discuss strategy.”

Ms. Dyson goes on to explain her motives for becoming one of the “First 10”:

1. She wants to show that there’s nothing especially magical about her genome – she’s actually more worried about releasing the questionnaire, which documents her behavior!
2. She doesn’t have any deep secrets or vulnerabilities;
3. She won’t get fired and she has insurance (i.e. low potential for discrimination);
4. She wants to examine the effects of personal genome sequencing on society;
5. She believes such sequencing is inevitable, and;
6. The project will generate useful data for others to use.

There is a great discussion of the project and Ms. Dyson’s decision to join it in the comment section of a post at Genome Technology. You can also find more at EyeonDNA.