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Y Chromosomes of Prehistoric People Along the Yangtze River

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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:

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The Celebrity Genome Debate Rages On

Jason Bobe over at The Personal Genome has a great post this week called “False Alarm: The Celebrity Meme” about the use of ‘famous’ scientists in early genome sequencing.  He poses a number of interesting and thought-provoking questions about the topic.  Make sure you read the comments that others have left.  Hsien at EyeonDNA wrote so much that she made her answers a full-length post.

The subject is traveling all over the blogosphere.  The Rocketfish Manifesto addresses personal genome sequencing with a little bit of humor.  And John Hawks’ Anthropology Weblog has a lengthy post with some new insights.  There is a lot of great reading material available if you’re interested in the Personal Genome Project.

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Ethical and Legal Issues Surrounding Large-Scale Genomic Databases

I recently came across a review article by Henry T. Greely, a Professor of Law, Professor (by courtesy) of Genetics, and Director of the Center for Law and Bioethics at Stanford.The article is entitled “The Uneasy Ethical and Legal Underpinnings of Large-Scale Genomic Biobanks (pdf)” and was recently published in the Annual Review of Genomics and Human Genetics.

According to Mr. Greely, the identity of participants in large-scale genomic biobanks cannot effectively protected.A biobank is defined as a database of genotypic and phenotypic data.Using genetic information, physical information, or a combination of the two, people can identify an individual in such a large database:

“Someone really interested could get a DNA sample from me – from a licked stamp, a drinking glass, or some tissue – and have it genotyped for a few hundred dollars, but few will have to go to the genomic data; the phenotypic and demographic data will often be sufficient.”

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The Phylogeography of African Brazilians

southamerica2.jpg 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.

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Genetic Genealogy in the News

A couple of interesting news articles from Megan’s Root World:

  1. Megan’s post, An Avoidable DNA Error, comments on the mistaken identification of an infant who died on the Titanic. As it turns out, the mistake was due to dental error, NOT to genetic genealogy – see Megan’s follow-up post, Blame the Dentists!
  2. Megan and the Genealogue mention an article in The New Republic about The Genealogy Craze in America.
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Analysis of the name ’23andMe’

23andme.pngAs you all know, I have high hopes for the genetic profiling company 23andMe. Although 23andMe has not officially launched a product available to the public, it turns out that the founders have chosen a great name for their company.

Nancy Friedman, a name developer and corporate copywriter based in Oakland, has written a lengthy analysis of the name ‘23andMe’ on her blog ‘Away with Words.’She suggests that the name was deftly crafted and is even better than the oft-suggested name ‘46andMe.’Ms. Friedman’s post is also the first place I’ve ever seen a pronunciation for Anne Wojcicki’s last name (which is wo-JIT-skee).Turns out I wasn’t too far off!

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The Personal Genome Project’s “First 10″

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

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Finnish Genealogy and Evolution

 

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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.”

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Esther Dyson and the “First 10″

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.

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