Genetic Genealogy in the Classroom


Forty advanced placement science students at Soldan International High School in St. Louis have submitted their DNA for testing with the National Geographic Society’s Genographic project. An article in the St. Louis-Post Dispatch highlights some of the statements made by the students and faculty:

“Many times students don’t see the relevance of what they’re learning,” said Assistant Principal Alice Manus, the Soldan project coordinator. “What they’re learning here will have all sorts of relevance because, really, we’re looking into their lives.”

One student, named John, had more reason to be excited about this test than most – his father died when he was only 13. “I never knew him that well,” said the Soldan sophomore. “Maybe this will tell me more about who he was and where he came from.”

... Click to read more!

Genetic Genealogy Eliminates Two As Descendants of Joseph Smith

Update: Ugo Perego is not affiliated withh the website mentioned in the last two sentences.

Did Joseph Smith father children with any of his plural wives? The Deseret News has a lengthy article about recent efforts by a geneticist to answer the long-debated question about the founder of the Latter Day Saint movement.

Ugo Perego, the director of operations at the Sorenson Molecular Genealogy Foundation, has used genetic genealogy in an attempt to identify or rule out potential descendants of Smith. In 2005, Perego showed that three males were not descendants of Smith, and new testing has shown that two more alleged descendants of Smith are not his true descendants.

In order to rule out descendants, it was first necessary to characterize the Y-DNA thought to belong to Joseph Smith. According to the article:

... Click to read more!

DNAPrint and Bioserve – 600,000 Genetic Genealogy Tests

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.”

... Click to read more!

The Early Stages of the Genetic Genealogy Revolution – Part II


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.”

... Click to read more!

The Early Stages of the Genetic Genealogy Revolution


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.

... Click to read more!

Native American mtDNA from Chewing Gum and Textiles

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).

... Click to read more!

Beothuk DNA in Newfoundland

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.

... Click to read more!

Y Chromosomes of Prehistoric People Along the Yangtze River


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:

... Click to read more!

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.

... Click to read more!

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,, 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,, 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

... Click to read more!