More information from Spencer Wells on Geno 2.0

Dr. Spencer Wells provided me with additional information on Geno 2.0 again today, including a link to a recently published interview with him in BioArray News on GenomeWeb, "National Geographic to Use Illumina Chips in Next Phase of Genographic Project". You must register to read the article, but it is free to do so.

In the article, Dr. Wells discusses the community aspect of the new Geno 2.0 and emphasizes that although Geno 2.0's focus is on learning about one's ancestral origins, the test will support genealogical goals:

While National Geographic's project is focused on offering participants the ability to learn more about their deep ancestry, it will support genealogical activities, Wells said.
As it has done to date, National Geographic will allow Genographic participants to transfer their results to Family Tree DNA for free, where they will be able to network with other researchers. Additionally, they can opt to join a National Geographic-sponsored online community of Genographic participants to share their results. And, Wells noted, National Geographic will make participants' results free to them to download. 

He also clarifies Family Tree DNA's role:

Wells said that testing will be done at Family Tree DNA's Genomics Research Center in Houston. He noted that while Family Tree DNA helped design the chip and is processing the samples, Geno 2.0 remains a National Geographic project.

Perhaps, most importantly, the story quotes Dr. Wells' restating his belief that the raw data should always be returned to the customer:

"Your data belongs to you," he said. "We feel that this is a cornerstone of ethical DTC genetic testing."

I took this opportunity to ask him a couple of questions that I have received from readers:

Q: Will the Walk Through the Y customers whose samples were used for vetting the new chip receive their results?

A: Yes, the WTY and whole-mtDNA genome customers used in the validation process will receive their results when the results section of the website goes live for all Geno 2.0 participants this fall. As I said in the story, your data belongs to you.  There will be no charge to them for this, and we hope that they enjoy the new Geno 2.0 experience and will become cheerleaders for the project.

I am so happy to hear this news that the participants whose samples were used for vetting, including the mtDNA full sequence samples, will receive their results in concordance with Dr. Wells' belief that your data belongs to you.

Q: Can you comment on the inclusion of Native American samples in your research for Geno 2.0?

A: We have genotyped lots of Native American samples, though most are admixed to various degrees.  The reference populations were drawn from 1000 Genomes samples, as well as samples collected by the Genographic team in Mexico, the Caribbean, and South America, and we'll be expanding our reference set over the next year.  I don't want to discuss the analytical methods in detail until we finish writing the papers, but we have developed an innovative way of analyzing admixture that is capable of distinguishing Native American ancestry very accurately.

This is all for now, but I have no doubt, we will be hearing more about Geno 2.0 very soon.

News from 23andMe and FTDNA at SCGS 2011 Jamboree

I attended the lectures of 23andMe's Joanna Mountain and FTDNA's Bennett Greenspan at SCGS 2011 Jamboree, as well as participated in the ISOGG meeting's panel discussion. Below are some interesting tidbits that I learned while there.

23andMe News and Tidbits: 
23andMe recognizes Relative Finder as the company's most engaging feature. This is good news for customers interested in Ancestry tools. In the coming weeks at 23andMe, Relative Finder will undergo the following key improvements:
1.  23andMe will be launching a new interface for Relative Finder. It will display the birthplaces, current locations and ancestral locations (if provided) of anonymous matches. (I am told that I will be a beta-tester, so I will post screenshots when/if that happens.)
2.  23andMe customers will be able to sort their matches by mtDNA and Y-DNA haplogroups, most likely by the end of the month.
3.  23andMe customers will be able to report confirmed relationships for their predicted matches.

23andMe just had a paper on their Parkinson's Disease research accepted for publication in PLoS Genetics. (No news on publication date yet.)

23andMe's total number* of individuals likely to self-identify as:
1000 African American
3500 Latino/Hispanic
5500 East Asian
3400 South Asian
4900 Southern European
6200 Ashkenazi Jewish
56,000 Northern European
1,000 First generation from two continents
*These numbers are as of April 2011 and, obviously, approximate. JM-"In general, these are non-overlapping sets, but there are some individuals who do not fall into any of these categories."

Slide presented on June 11 at SCGS  Jamboree 2011
Courtesy Katherine Borges

Joanna is "very optimistic" about the future of full sequencing for the Y-chromosome and expects it to happen "very soon", however 23andMe has no plans to offer a separate Y-chromosome sequencing product.

FTDNA News and Tidbits:
1.  The 2011 FTDNA DNA Administrator's Conference will be held November 5th and 6th in Houston.
2.  FTDNA has found previously undiscovered mutations in ~10% of all new Full Sequence mtDNA samples.
3.  FTDNA sold 200 "Walk the Y" tests during their last sale. So far they have completed 100 of these samples and found 140 new SNPs. The "Walk the Y" tests take five times more plate space than the Full Sequence mtDNA tests. As a result, FTDNA can run only two of these tests per day.
4.  FTDNA is still planning to allow uploads of 3rd party data to their Family Finder database. (Very soon!)
5.  FTDNA has shipped out over 207,000 kits since inception and 406,000 kits have been sold by National Geographic. FTDNA has 208,000 unique Y-DNA results and 128,703 unique mtDNA results in their database.
6.  FTDNA's Population Finder uses 64 reference populations.

I hope you learned something new. I know I did!

[Disclosure - My company StudioINTV has an existing production agreement with FTDNA that has no bearing on the opinions I express. I also receive a small commission from FTDNA on non-sale orders through my affiliate link, which I use to fund DNA tests. I receive no other compensation in relation to any of the companies or products referenced in my blog.]