The Genetic Genealogist

I’ve added a new page to the blog called “Featured Articles“. It’s available 24/7 at the top of every page, and contains a categorized list of about 50 of my favorite articles from the last year. These posts are listed under categories including “Popular Articles”, “Personal Genomics”, “Learning About Genetic Genealogy”, “Ethical Issues”, and “Famous DNA”. This easy-to-read format is much easier to navigate than the clumsy “Categories” column in the right sidebar, which returns too many results in no apparent organization. If you’re relatively new to The Genetic Genealogist, you might find some interesting articles that you missed the first time around. Happy reading!

An Updated Y-DNA Tree at ISOGG

The International Society of Genetic Genealogy (ISOGG) announced today that their Tree Team has completed the 2008 version of the Y-DNA Haplogroup Tree. This revision was a major undertaking, because, as ISOGG states in the version history, “[t]he Karafet et al paper (2008) required a significant revision to the tree and affected all haplogroups.” The reference for this paper is (Karafet T M, Mendez F L, Meilerman M B, Underhill P A, Zegura S L, Hammer M F, (2008).
New Binary Polymorphisms Reshape and Increase Resolution of the Human Y-Chromosomal Haplogroup Tree. Abstract. Genome Research, published online April 2, 2008. Supplementary Material.). From ISOGG’s official release:

MAY 04, 2008 – The 2008 version of the ISOGG Y-DNA Haplogroup Tree is now available online: http://www.isogg.org/tree/. New to the tree is a haplogroup conversion table which is downloadable in MS Word. If you do not have MS Word/MS Office, you can download openoffice.org for a compatible word processing program. Appreciation goes to Richard Kenyon and Charles Moore for their work on compiling this table.

Thanks to Alice Fairhurst and the entire ISOGG Tree Team for all of their hard work and dedication. Added thanks for consultation goes to Jim Wilson, Dennis Garvey, Ken Nordtvedt, and Natalie Myres on various haplogroups. Additional appreciation to Charles Moore (Hg D) and Vincent Vizachero (Hg R) for joining the Content Team Experts.

The site also has a Haplogroup Conversion Table (MS Word) to convert a 2007 haplogroup to an updated 2008 haplogroup.

Updates at FTDNA and ySearch

The Karafet et al paper also resulted in updates to haplogroup designations at Family Tree DNA and ySearch. Users who have tested their Y-DNA through FTDNA or have created a profile at ySearch automatically had their haplogroup designation updated this morning (May 5th, 2008). For instance, before the update my haplogroup was R1b1c9a. After the update, the haplogroup is called R1b12a1c.

New Deep Clade Tests Reflects Changes

As a result of the SNPs analyzed in the Karafet et al paper, Family Tree DNA has updated their “Deep Clade” SNP tests. From the official announcement this morning:

New SNPs and haplogroup branches have been discovered and published, which have now been integrated into the Deep Clade testing panels. Customers who are currently waiting for Deep Clade test results will automatically be upgraded to the new testing panels at no additional fee. Participants who previously ordered Deep Clade tests and for whom some new SNPs may be informative will be offered a Deep Clade test extension, as applicable.

The new Deep Clade testing system is designed to determine a participant’s placement on the haplogroup tree. The test begins with their predicted haplogroup and tests whatever SNPs are necessary in order to determine their haplogroup assignment on the tree. Results of all SNPs tested are reported to the customer as they are completed.

Deep Clade tests are available for haplogroups E1b1b, G, I, J, and R (includes R1a, R1b, and integrates the U series SNPs within R1b).

To order the test, FTDNA users should check under the “Haplogroup” page on the left side of their personal page. Note that the FTDNA tests do not incorporate all the SNPs used by the ISOGG Tree Team to create the updated 2008 Y-DNA Tree. The ISOGG tree uses some SNPs that are new, provisional, or private and are not yet used by testing companies.

Although the genome scanning services offered by companies such as 23andMe, deCODEme, and SeqWright have been front and center in the press the last few weeks, I’m sure that the following information will not be included in any of the reports.

Comparisons

Two different sources have concluded that the scanning service offered by 23andMe and deCODEme, who use different types of Illumina SNP Chips, are highly reproducible. In January 2008, Ann Turner compared the results of testing at deCODEme and 23andMe, and concluded that of the 560,163 SNPs that overlapped and had a “call” (meaning there was a measurable result), they agreed on 560,128 and disagreed on 35. Ann wrote in January:

In all of [the disagreed calls], one company would make a homozygous call while the other company made a heterozygous call – there were no cases where they made a completely discordant call. All in all, I’d say that is pretty impressive.

The second analysis comes from Antonio C B Oliveira at Longa Vista, a new blog that appears to have been created to present these results and related information. Oliveira obtained results from 23andMe and deCODEme and compared the results, which are available here. He concluded that of the 560,299 SNPs that overlapped and had a call, the two scans agreed on 560,276 and disagreed on 23. The 23 disagreed upon SNPs are listed by chromosome. Oliveira writes:

This error rate seems to me to be quite acceptable and I wonder if this is the rate expected in scientific studies using the same technology.

Program to Compare Your Results

Interestingly, Oliveira created a computer program to analyze the results for him, and he has graciously made that program available “as a Windows executable and the source code is provided under the GNU General Public License.”

Conclusions/Thoughts

Note that Oliveira’s results contained 136 more overlapping results, presumably because of fewer no-calls in the data. Is Illumina able to produce more calls as they gain experience with the process, or is this an expected amount of variation from person to person? I would be interested to see more results and comparisons to determine the answer to this question.

HT: Genetic Future. If you’re interested in genome sequencing or personalized genomics, you should be reading Genetic Future. I highly recommend adding the feed to your reader. Genetic Future gave a hat tip about this information to Kevin Kelly at The Quantified Self. There, Kelly points out that none of the SNPs in Oliviera’s analysis are currently associated with any physical phenotype or disease. I hope Kelly plans to do a comparative analysis of his results, as that would be an interesting addition to the information provided by Turner and Oliviera.

Last week I received a press release announcing the creation of a non-profit organization to raise and disseminate funds to increase original research in genetic genealogy testing (some of which will undoubtedly be reported in the open-source Journal of Genetic Genealogy). The DNA Fund also has a blog, available here. Following is the press release:

SALIDA, CA – The DNA Fund, (www.dnafund.org), a new non-profit organization has been established to fund DNA testing scholarships and grants for ancestral DNA studies. Currently in Phase 1 of the Fund’s launch, testing monies will be raised through fundraising affiliates. Scheduled for Phase 2, the Fund will accept donations and in Phase 3, coordinate grants for DNA projects and studies.

“DNA testing is usually considered a luxury item, but the knowledge that it provides is invaluable. The goal of The DNA Fund is to test as many people as possible and share the information in the public domain through publications and databases.” says DNA Fund President, Katherine Borges. “People can support The DNA Fund just by using our affiliates for their normal shopping habits. The affiliates give a percentage of the purchases back which can be channeled into DNA testing funds.”

The DNA Fund is the first entity of its kind to provide funding for public genetic genealogy projects and other ancestral DNA studies.

Some of the projects proposed by The DNA Fund for funding include:

• Eastern/Balkans/Middle East R1b 67-100 STR marker haplotypes of a small sample of the rarer clades via upgrades and also fully SNP tested.
• Mitochondrial DNA analysis of Punjabi population of Pakistan.
• Hungarian-Bukovina Y-chromosome testing.
• Investigating the Phylogeny of mtDNA Haplogroup T based on Full mtDNA Sequences
• SNP research of internal branching within Haplogroup F, along branches leading to [IJ] and G