2

Reconstructing the Worldwide Family Tree

I first saw mention of Mike Elgan’s story, “Coming Soon: The Mother of All Genealogy Databases” at Jasia’s Creative Gene (The Google Family Tree?), and then I saw it at the Genealogue (NothingWill Save Us From Boredom).

In the article, Mr. Elgan imagines an enormous future database that combines traditional genealogical records and DNA to link everyone together.  Two individuals could then, for instance, search the database to find their closest relationship to each other.  My first thought, of course, is of privacy issues and plain old bad genealogical data (of which the internet is full).

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The Early Stages of the Genetic Genealogy Revolution – Part II

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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.”

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DNA to the Genealogical Rescue, Again

In today’s Washington Post there’s a story about The Boy in the Iron Coffin.This coffin was accidentally discovered by a construction crew in Washington, D.C. in 2003.Research conducted by the Smithsonian’s Museum of Natural History discovered that the body inside, still wearing a white burial suit, was that of William T. White, about age 15.William, who appears to have had a heart defect that would have made him sickly, died on January 23, 1852:

“The boy was extremely well preserved and clad in white cotton clothing that included a pleated shirt and vest with cloth-covered buttons, flared trousers, darned socks and ankle-length underdrawers.”

According to the article, the body “had been buried in a cemetery that probably belonged to Columbian College, the precursor to George Washington University, in what is now Columbia Heights, and had been a student at the college preparatory school when he died.”

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Sorenson Molecular Genealogy Foundation Collects Panamanian DNA

On the heels of last week’s announcement that Sorenson Molecular Genealogy Foundation (SMGF) will be collecting DNA samples in Mongolia comes new information that the company will be conducting a similar project in Panama.

According to the announcement, SMGF has partnered with the Gorgas Memorial Institute (Instituto Conmemorativo Gorgas de Estudios de la Salud Panama) and will attempt to collect 1,500 to 2,000 DNA samples with pedigree charts.The project will gather DNA from each of Panama’s nine provinces and three territories and will include individuals from all major ethnic groups, and from both urban and rural areas:

“We are honored to join with Gorgas Memorial Institute, Panama‘s primary institute for health and population studies, to study this country’s diverse, multi-faceted populations,” said Dr. Scott Woodward, executive director of the Sorenson Molecular Genealogy Foundation. “Panama is a fascinating melting pot, its genetic and cultural mix having been influenced by a broad array of Native American populations, Africans from the slave trade, and Europeans and Asians from multiple eras.”

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Genetic Genealogy Spreads Around the World

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Commercially available genetic genealogy isn’t just for Americans and Europeans anymore. Eastern Biotech & Life Sciences, centered in Dubai, recently sent me an email announcing their new venture into the field of genetic genealogy testing.

Although it wasn’t apparent from the email that I received, Eastern Biotech & Life Sciences has partnered with Family Tree DNA to offer genetic genealogy testing. The following sentence comes from a press release at i-newswire: “Eastern Biotech & Life Sciences is proud to be associated with Family Tree DNA to create a database for the Middle Eastern population.”

From the Email:

“Dubai: 09/12/2007-Eastern Biotech & Life Sciences is set to launch a new Wall Chart of DNA Ancestry services to the people of the Middle East to help them invent their deep ancestors from 150,000 years ago. The roots of this tree lie more than 100,000 years in the past, at a time when our hunter-gatherer ancestors were living in Africa. As the branches of the tree multiply, they record the history of our species and the dramatic stories of how pioneering groups of humans explored and populated our planet. The different journeys they made shaped the world we know today.

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DNA Collection Project in South Africa

Dr. Wilmot James, head of the African Genome Project and honorary professor of human genetics at the University of Cape Town, is heading a DNA collection project in South Africa.Dr. James is joined by his colleague Himla Soodyall, a scientist at the National Health Laboratory Service and an associate professor in the Division of Human Genetics at the University of Witwatersrand.On September 9th, James and Soodyall collected swab samples from a number of Capetonians.

The African Genome Project is supported by the South African genealogy website Ancestry24.com (although I was not able to find any information there).One of the goals of the project is to create a public genetic database to examine “how the country became populated over thousands of years” by filling in the gap in current DNA databases.

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What’s on the Web?

  1. Misha Angrist wrote about the implications of personal genome sequencing in “Warts and all.”

  1. I think most everyone would agree that affordable whole-genome sequencing will be around long before we understand the information it reveals.I asked another member of The DNA Network, The Gene Sherpa his opinion on the matter.Genome Technology Online also thought it was an interesting discussion.And by the way, the Genome Technology Online’s daily newsletter is a great way to stay up-to-date.

  1. DNA Consulting is launching an online forum called DNA Ancestor Communities (from Family Tree Magazine).

  1. At Venturebeat: lifesciences, David Hamilton wrote a great post about genome sequencing and insurance – “Personal genomics and the end of insurance.”It received a lot of attention this week, including a mention in Dick Eastman’s Online Genealogy Newsletter.

  1. EyeonDNA has a clip of Craig Venter from the Charlie Rose show in 2000, back before Venter was able to browse his entire genomic sequence.

  1. Jay Flatley of Illumina revealed more information about future products being offered by 23andMe.Naturally, it received a lot of attention (be sure to read the comments as well):

oI wrote about it here at The Genetic Genealogist;

oVentureBeat: lifesciences wrote an article, and ended with: “Rumors of yet a third, still stealthy, personal-genomics startup are also swirling around the Valley.”Any ideas?

oAnother early mention came from Megan’s Roots World, who, like me, picked up on the fact that 23andMe is initially focusing on ancestry.

obusiness|bytes|genes|molecules wrote an interesting post.

oGigaOM has a very brief mention.

oGenome Technology Online links back to the Forbes article as well.

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23andMe Partners with Illumina – To Offer Genetic Genealogy?

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23andMe has been the subject of much discussion in the biotech and personalized medicine circles of the blogosphere (See here, here, here, here, here, here, here, and here for plenty of information/speculation/discussion).

In August, 23andMe announced (“23andMe and Illumina Forge Consumer Genomics Goliath”) that they have partnered together to offer “consumer genotyping” – more about that in a minute.Illumina produces “SNP chips”, chips that can test a genome for thousands of SNPs (single nucleotide polymorphisms) at a time.For example, the company has one chip that tests one million SNPs for as little as $600, and another chip that tests 550,000 SNPs (the HumanHap550) for only $300-$450.Interestingly, Illumina is also able to custom build chips to add specific SNPs if the customer so desires.Additionally, as the announcement touted, Illumina is also exploring the world of inexpensive whole-genome sequencing, suggesting that this partnership with 23andMe could transition from cheap SNP testing to cheap whole-genome sequencing at some point in the future.

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A Meeting of the Minds

If you’re interested, here’s a link to a document from the Edge Foundation, a group designed to promote the discussion of intellectual pursuits. The document is a summary (including video links) of a casual meeting between some fantastic scientific minds (Craig Venter, Freeman Dyson, Robert Shapiro, Dimitar Sasselov, and Seth Lloyd) which took place in late August.

Although Dr. Church doesn’t discuss the Personal Genome Project, his brief discussion about our past and our future is very interesting.  There’s also a summary of the meeting from Gregory T. Huang, an invited journalist.  I see that one of the invited guests was Ting Wu, a researcher at Harvard who has initiated the pgEd (personal genetics education project).

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Dr. Kirk M. Maxey Shares his Expertise with Members of the DNA-NEWBIE Mailing List

The DNA-NEWBIE mailing list is a great resource for people who are new to genetic genealogy or genetic testing in general. The list provides a forum for questions while promoting education and the sharing of ideas. I primarily use the mailing list to follow current trends or concerns in the field of genetic genealogy so that I can share them here on the blog.

The recent deluge of media attention regarding J. Craig Venter’s diploid genome sequencing prompted one list-member to quote Dr. Edward Rubin: “It’s not clear whether it’ll be 10 years or 50 years, but in our lifetime, [individual DNA sequencing ] will happen.” The list-member goes on to say that it will probably not happen in his lifetime since he turns 75 next month.

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