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The Full mtDNA Genome of Ötzi is Sequenced (Twice?)

Großglockner seen from the southwest. The Groß... Image via Wikipedia Ötzi the Iceman is the popular name for a 5,000 year-old mummy discovered frozen in the ice of the Alps in 1991.  Studies of the Iceman has revealed an immense amount of information about him, including details of his life, his death, and his culture.  Although Ötzi’s mtDNA has previously been studied, researchers had only examined short segments which suggested that his mtDNA belonged to Haplogroup K.  A new paper in Current Biology (subscription only darn it) details Ötzi’s full mtDNA genome for the first time:

"Using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products, we have retrieved the first complete mitochondrial-genome sequence of a prehistoric European. We have then compared it with 115 related extant lineages from mitochondrial haplogroup K. We found that the Iceman belonged to a branch of mitochondrial haplogroup K1 that has not yet been identified in modern European populations."

The full sequence (which has been deposited in GenBank with accession number EU810403) was then compared to 115 published full mtDNA Haplogroup K sequences.  The comparison suggests that Ötzi belonged to a previously uncharacterized … Click to read more!

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The Retail DNA Test Named the #1 Invention of 2008 by TIME Magazine

Image representing 23andMe as depicted in Crun...
Old 23andMe logo via CrunchBase

The latest issue of TIME Magazine lists the top 50 inventions of 2008, and the invention of the year is the Retail DNA Test.  The article is mostly about the product currently offered by 23andMe.  From the article:

“We are at the beginning of a personal-genomics revolution that will transform not only how we take care of ourselves but also what we mean by personal information. In the past, only élite researchers had access to their genetic fingerprints, but now personal genotyping is available to anyone who orders the service online and mails in a spit sample. Not everything about how this information will be used is clear yet — 23andMe has stirred up debate about issues ranging from how meaningful the results are to how to prevent genetic discrimination — but the curtain has been pulled back, and it can never be closed again. And so for pioneering retail genomics, 23andMe’s DNA-testing service is Time’s 2008 Invention of the Year.”

As the past year has shown, many people are opposed to this type of product for various reason, including that the test doesn’t involve genetic counseling, it isn’t ordered or interpreted by your personal doctor, and issues of genetic discrimination.  However, the article doesn’t shy away from these issues and provides a brief but interesting look into both sides.

This award highlights the fact that we are in the midst of a vast genetic revolution.  We are the first generation to be able to peer into the DNA inherited … Click to read more!

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Another Consideration For Genetic Sequencing and Privacy

James Watson (February, 2003)
(Jim Watson via Wikipedia)

As if there wasn’t enough to worry about during the genetic revolution, researchers have found a way to characterize redacted genetic sequences from whole-genome or large-scale sequencing.

Here’s how it works.  Let’s say that Mr. X has had his genome sequenced, but doesn’t want to know the results of some genes known to influence the development or progression of Alzheimer’s Disease.  So when he receives his genomic sequencing, these genes have been ‘redacted’, or removed from the data.  This is exactly what James Watson decided to do when he received his data.

Characterizing Redacted Genes

However, researchers have characterized one of Watson’s redacted genes by examining the sequences surrounding the gene in question.  … Click to read more!

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Genetic Genealogy Tidbits

Image created by Abizar Lakdawalla - fair use.
Image via Wikipedia

This week I was quoted in the November issue of Wired Magazine about the use of autosomal DNA for genetic genealogy testing.

A Controversy

At “Adoptees use DNA to find surname,” Larry Moran at Sandwalk comments on my recent articles (here, here, and here) regarding the use of genetic genealogy (or genetic sequencing in general) test results to find unknown biological parents.  Although Dr. Moran accuses me of being a “cheerleader” who is blind to any ethical concerns associated with using DNA to find biological parents, he obviously didn’t do his research!  Less than a month ago I wrote this on the blog:

“For most people, being able to identify your own ancestors based on your own DNA poses few if any ethical dilemmas. However, what if your neighbor or your stalker or even law enforcement wants to use a sample of your DNA to identify your ancestors? Additionally, what if your living ancestor doesn’t wish to be identified? Does the ancestor have that right, or is possible identification through genetic genealogy just one of the consequences of parenting a child anonymously or simply having sex with another person?”

In response to a write-up at Genome Technology, Discovering Biology in a Digital World wrote “Hey sperm donors, could DNA testing be hazardous to your wealth?“.

Blending Genetic Genealogy and Personal Genomics

Often, articles that discuss both genetic genealogy and whole-genome scans … Click to read more!

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More On Revealing Surnames Using Genetic Genealogy

DNA
Image by gravitywave via Flickr

Last week I wrote about using genetic genealogy databases to identify someone’s surname (see “DNA Could Reveal Your Surname, Of Course.”)  The article discussed results from researcher Dr. Turi King which suggested that there is a 24% to 50% chance that two men who share the same surname share a common ancestor through that name, with chances increasing if the surname is rare.

Somehow I completely missed “Adoptees use DNA to find surname“, an article at BBC News this June.  Men who were adopted as children are using genetic genealogy databases in an attempt to identify their biological surname.  This is Dr. King’s research in motion.  Family Tree DNA, for example, has a project for Adopted people that is over 2 years old, and has a success rate of more than 30%, thanks in large part to their database … Click to read more!

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DNA Could Reveal Your Surname, Of Course

allelic length variation among 6 individuals
Image via Wikipedia

New research from Mark Jobling’s lab at the University of Leicester suggests that Y-DNA can be used to determine a male’s surname.

I know, I know, this is obvious to anyone who is familiar with genetic genealogy.  Just check out the many instances of this type of determination at ISOGG’s Success Stories website, for example.  However, as you’ll see below, this research has resulted in some new and interesting information.

Method

Dr. Turi King, who conducted the research, recruited over 2,500 men with roughly 500 different surnames to submit Y-DNA samples.  The sample set included a group not sharing surnames as well as sets of men (between 2 and 180) who shared a surname (including recognized variants).  She then typed 9 SNPs and 17 STRs.  There’s much … Click to read more!

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Article Review: “Bio Science: Genetic Genealogy Testing and the Pursuit of African Ancestry”

I just finished reading an article by Alondra Nelson in the journal Social Studies of Science entitled “Bio Science: Genetic Genealogy Testing and the Pursuit of African Ancestry” (Social Studies of Science 2008 38: 759-783).  Dr. Nelson is Assistant Professor of Sociology, African American Studies and American Studies at Yale University.

This very interesting and insightful article aligns with my own premise, which I’ve stated previously, that receiving the results of a genetic genealogy test is only the beginning of the journey for any individual interested in their own identity or genealogy.

Based on her research in this area, Dr. Nelson writes about the complex interpretation of the results of genetic genealogy testing by African-Americans and black British.  Rather than completely altering their preconceived … Click to read more!

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Personal Genome Project Begins Releasing Information

image The Personal Genome Project (PGP) was established to analyze and publicly share the genomes and personal information of up to 100,000 volunteers in order to advance understanding of “genetic and environmental contributions to human traits and to improve our ability to diagnose, treat, and prevent illness.”  In the first phase of the PGP, ten volunteers (the “First 10″ – see information about the First 10 here on my blog and at the PGP website) have had their DNA analyzed and have given their personal information.

Last month, George Church, the PGP’s principal investigator, reported that the project expected to publish data about the First 10 on its website in mid- to late October.  Church might have meant genotype (i.e. sequencing) information, since some information about phenotype, health … Click to read more!

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Complete Genomics Will Sequence Your Entire Genome for $5,000 Starting in 2009

Andrew Pollack at the New York Times wrote an article published today entitled “Dawn of Low-Price Mapping Could Broaden DNA Uses.”  The article is about a start-up company called Complete Genomics which will begin sequencing customer’s genomes for $5,000 starting in the second quarter of 2009.  From the article:

“Complete Genomics will not begin its service until the second quarter of next year. By then, the cost of competing technologies will no doubt have fallen further. Just last week, Applied Biosystems, a leading manufacturer, said it expected that its newest machine would allow a human genome to be sequenced for $10,000, although that includes only the cost of consumable materials, not labor or the machinery.”

The article next mentions Knome, which is still offering complete genomes for $350,000.  I expect that price to drop dramatically within the next few months.  Indeed, as the article points out:

“Complete Genomics will not offer a service to consumers. But it will provide sequencing for consumer-oriented companies like Knome.  Knome is already exploring farming out its sequencing to Complete Genomics. “We anticipate we’d be able to significantly drop our price,” said Jorge C. Conde, the chief executive of Knome, which is based in Cambridge, Mass.”

Interestingly, the company says that they are still making money at $5,000, and hopes to sequence a million genomes by 2013:

“Mr. Reid [the chief executive] said Complete Genomics hoped to perform 1,000 human genome sequences next year and 20,000 in 2010, with a goal of completing a million by 2013. That assumes the company can raise the money and find partners to build 10 sequencing centers at a cost of $50 million each. It also assumes there will be enough demand.”

Will there be enough demand?  What effect will this have on the cost of sequencing by other companies?  What effect will this have on the field of genetic … Click to read more!

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RootsTelevision Turns Two

Yesterday, RootsTelevision.com celebrated its two-year birthday.  RootsTelevision was created by Megan Smolenyak Smolenyak and Marcy Brown in 2006, and currently contains programs in 25 different channels!  You can read more about the site and about its creation at Megan’s Roots World.

You might remember that a few weeks ago I was interviewed by Dick Eastman for RootsTelevision.com, which was a terrific experience.  And don’t forget, you can stay up-to-date on RootsTelevision.com’s DNA Channel right here at … Click to read more!