Thursday 26 July 2012

Ancestry SNPs galore

Today sees the launch of  Geno 2.0, an exciting new DNA test which marks phase two of the Genographic Project, a scientific research project run by National Geographic in partnership with Family Tree DNA and IBM. The launch has been covered by a number of bloggers in America who attended the pre-launch presentation. They each cover the test from slightly different perspectives and all the posts are well worth reading.

- Roberta Estes     National Geographic Geno 2 announcement - the human story

- Roberta Estes     Geno 2.0 - Q&A with Bennett Greenspan
- CeCe Moore        National Geographic and Family Tree DNA announce Geno 2.0 

- Blaine Bettinger   National Geographic and Family Tree DNA announce Geno 2.0
- Judy Russell       Geno 2.0 launches 
- Emily Aulicino     National Geographic announces new DNA test
- Razib Khan        The Genographic Project: on to the autosome!

The new Geno 2.0 test is a deep ancestry test. It complements the existing DNA tests that are traditionally used by genealogists and does not replace them. The new test is looking at special markers known as SNPs (pronounced 'snips'). These markers can tell us how much of our DNA we share in common with other populations from around the world. Both males and females will discover their mitochondrial DNA haplogroup. Males will discover their Y-DNA haplogroup. Haplogroups represent branches of the human family tree. The inclusion of new SNPs in the Geno 2.0 test will allow scientists to define not just the branches of the family tree, but also the twigs (subclades) which make up those branches.

For surname projects we use a different marker known as a Y-STR marker. Y-STR markers are like the leaves on a tree and we use Y-STR tests to place the leaves on the tree by grouping matching results in genetic families. If you are a male and are interested in using a DNA test to help with your genealogy research you should take a Y-STR test with one of the many surname or geographical projects at Family Tree DNA.

The new Geno 2.0 test will, however, effectively serve as a replacement for the old Y-DNA deep clade test from Family Tree DNA which provided detailed subclade assignments. The old deep clade test looked at a small handful of SNPs and it was necessary to order new SNPs à la carte as and when they were discovered. For just a little bit more money the new Geno 2.0 test covers 12,000 Y-DNA SNPs all in one go, and includes many new SNPs that were not previously available. It is set to transform our knowledge of the Y-DNA haplogroups.

The Geno 2.0 test covers 3,200 mitochondrial SNPs (about 19% of the mitochondrial genome). If you are only interested in learning your mtDNA haplogroup assignment then you should take the Geno 2.0 test. If you are interested in using mtDNA for matches within a genealogical timeframe (within the last 400 years) or if you are interested in participating in mtDNA scientific research then you will need to order a full mitochondrial sequence (FMS) test from Family Tree DNA. The FMS test sequences the entire mitochondrial genome (100%) which consists of 16,569 bases.

It will be interesting to see how the new Genographic Project test impacts on the other SNP tests that are currently available. Autosomal SNP testing is currently offered by 23andMe, Family Tree DNA and Their tests look at many more SNP markers than the new Geno 2.0 test. 23andMe tests one million SNPs. Family Finder and Ancestry test around 700,000 SNPs, I have written previously about my experiences with the 23andMe test and the Family Finder test. Both these tests can be used to find matches with genetic cousins within the last five generations or so. The 23andMe test also provides information on health issues. have recently launched their own autosomal DNA test. I am currently waiting to receive my results, and will be reporting on this test in due course. The Geno 2.0 test cannot be used for cousin matching as it does not test enough SNPs to make confident relationship predictions so these tests will continue to be useful for genealogical purposes.

The new Geno 2.0 test will, however, be the test of choice for anyone interested in learning about their ethnicity. The existing autosomal DNA tests only provide very vague information on ethnicity giving percentages of Asian, European and African admixture. The Genographic Project, with the power of its huge database (524,000 tests from 140 countries) and the focus on ancestry informative markers, should in theory be able to provide highly detailed ethnicity breakdowns and they will effectively wipe out all the competition. This new test might hit Ancestry particularly hard. Ancestry have invested a huge amount of money in their new autosomal DNA test and have specifically targeted their test at the large American market, where there is a lot of interest in ethnicity testing. Despite the large investment the early reports suggest that there are many problems with the tests which have yet to be ironed out.

The British company BritainsDNA offers a deep ancestry SNP test which looks at just 200 Y-DNA and 200 mtDNA SNPs for £200 (no autosomal SNPs are included). In comparison the Geno 2.0 test covers 143,000 SNPs (including 12,000 Y-DNA SNPs and 3,200 mtDNA SNPs) and costs just $199.95  (£128). It is difficult to see how BritainsDNA can possibly compete with the Genographic Project.

Further details about the Geno 2.0 test can be found on the Genographic Project website. Pre-orders are now being accepted. If you try to place an order you are told that the kit will be shipped on 30th October 2012.

See also my blog post dated 18th August which provides additional information on Geno 2.0.  

© 2012 Debbie Kennett


Anonymous said...

Thanks for the informative 'review', Debbie, and the links.

As I am one of many who have already done all the FTDNA tests including deep clade, I guess I'll wait (as you suggest) to see what FTDNA offers to members.

I hope the NatGeo database of results is available for FTDNA member search/match purposes in due course, especially because of its world wide coverage.


Debbie Kennett said...

If you've already done the deep clade test and ordered lots of extra Y-SNPs it might not be worth doing this test unless you're interested in having the admixture breakdown. We need to wait until the publication of the paper later this year to find out which SNPs are included and how many new ones there are.

Debbie Kennett said...

I'm not sure how the matching database is going to work, but as kits are also being sold by FTDNA I would hope that it will be set up so that Genographic people can easily transfer their results to FTDNA. All the results from project will eventually be made publicly available.

Anonymous said...

I am interested in this 23andme test, because it tests a million snps, and at $99, its affordable. However, I have had deep clade, and ongoing snp testing, and not sure how results will transfer over, so not sure whether this test will be worthwhile or not.

Debbie Kennett said...

If you order the 23andMe test you can transfer your results to the FTDNA database with the third-party transfer program so that you can have access to Family Finder matches:

FTDNA has a more international database and that way you get the best of both worlds. If you've only done Y-SNP testing then it would be worthwhile.