In the past, scientists have primarily examined the mtDNA of ancient DNA.After all, mtDNA is much more prevalent (100â€™s to 1000â€™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 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 canâ€™t
reveal those time estimates, however, because I don’t have access to the article.
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.
Thereâ€™s a great recent article in Scientific American entitled â€œWhat Finnish Grandmothers Reveal about Human Evolutionâ€ highlighting the research of biologist Virpi Lummaa.Iâ€™ve mentioned before that while genetics is a useful tool for genealogical research, genealogy can also be a useful tool for genetic research!Dr. Lummaaâ€™s research does exactly that.
Dr. Lummaa used 200 years of genealogical records to study the influence of evolution on reproductionâ€
â€œThe 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.â€
Esther Dyson is a prominent force in the digital world, and is considered to be a member of the â€˜digeratiâ€™ (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 â€œFirst 10.â€
The â€œFirst 10â€
The â€œFirst 10â€ (or â€œFirst Tenâ€) 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 â€œmasterâ€™s level or equivalent training in genetics or equivalent understanding of genetics research.â€According to the PGP website, â€œ[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.â€According to a recent New York Times article, the â€œprojectâ€™s volunteers will receive the one percent of their genome currently deemed most useful at a cost of $1,000.â€This conflicts with the PGPâ€™s description of the cost, and Iâ€™m not sure what the discrepancy is about.
Some interesting posts about DNA and/or genetic genealogy in the blogosphere:
Dr. Mark A. Jobling at the University of Leicester published a study in 2005 that examined DYS464, a Y-DNA marker commonly sequenced for genetic genealogical purposes.As it turns out, sequencing DYS464 can inadvertently detect an AZFc deletion.Deletion of AZFc (azoospermia factor c) causes spermatogenic failure and subsequently, male infertility.This marker is tested by at least 6 firms.
Dr. Jobling pointed out that a previous study had concluded that an AZFc deletion could be found in 1 in every 4000 males.In Dr. Joblingâ€™s study there were 3 cases in 3255 males tested, which he states is â€œnot significantly different from 1 in 4000.â€A story in the New Scientist stated that â€œa study by Jobling’s team suggests that 1 in 1000 men has the deletion,â€ but I think that is an overstatement by the media. I havenâ€™t seen anywhere that Dr. Jobling made such a statement – he was merely listing some of his data. Elsewhere, Ann Turner has suggested that at FTDNA, the number is around 1 in 8,000.Although the exact frequency has not yet been determined, it appears that it is rather low.
My great-grandmother belongs to Haplogroup H, and I always feel a little bad for her.Not that I have anything against Haplgroup Hâ€™ers, but they got the short end of the stick.You see, currently all mtDNA sequences are compared to the Revised Cambridge Reference Sequence (rCRS), an mtDNA sequenced derived in the early 1980â€™s and recently updated.Since the source of most of the mtDNA for that sequence belonged to Haplogroup H, people who belong to Haplogroup H often have no deviations at all and their sequencing results tend to be a little boring.Imagine if your mtDNA testing company sends your results and they say: â€œYou belong to Haplogroup H, and your deviations from the rCRS are as follows: 0.â€You see, a little dull.
A recent paper in the American Journal of Physical Anthropology examined mtDNA extracted from the hair and nails of eight Inuit mummies. These essentially freeze-dried mummies were discovered in 1972 in a natural tomb at Qilakitsoq in the Uummannaq Municipality of Greenland. Using C14 analysis, the mummies have been dated to approximately 1460.
The bodies were found in two separate positions about 1 meter apart. In Grave I, there were five bodies:
- I/1 = Male Infant #1 – about 6 months of age
- I/2 = Male Infant #2 – about 4 to 4.5 years of age
- I/3 = Female #1 – about 20-25 years of age
- I/4 = Female #2 – about 25-30 years of age
- I/5 = Female #3 – about 40-50 years of age
In Grave II, there were 3 bodies:
- I/6 = Female #4 – about 50 years of age
- I/7 = Female #5 – about 18-21 years of age
- I/8 = Female #6 – about 50 years of age
The researcher’s primary goals were to sequence the HVR1 region of each individual’s mtDNA, and then to compare the results to determine possible relatedness of the remains. All 8 individuals fell into Haplogroup A2, but belonged to three different maternal lineages which were mixed between the two grave sites:
The BBC has an article about genetic genealogy testing of nine celebrities in Brazil for a project called Afro-Brazilian Roots by the Brazilian Service of the BBC. These lucky individuals received Y-DNA, mtDNA, and autosomal testing, and most were surprised with the large proportion of European genealogy revealed by the tests.
“Brazil has more people with black ancestry than any other nation outside Africa, and its mix of Indians, Africans and Europeans gave rise in the past to the claim that the country was a ‘racial democracy.’ ”
“No one is pure in Brazil. That’s why the country has the face of the future,” said Harvard Professor Henry Louis Gates Jr., coordinator of a similar project in the U.S.”