SNP testing is required to confirm haplogroup assignments, to learn more about your deep ancestry and to rule out false positive matches. Y-SNP chip tests are available from the Genographic Project and BritainsDNA. More comprehensive sequencing tests using next generation sequencing technology are available from Full Genomes Corporation and Family Tree DNA. Single SNPs can be ordered from Family Tree DNA and YSEQ.
For advice on SNP testing consult the project administrator of the relevant Y-DNA haplogroup project.
There are currently two companies that offer single SNPs.
Family Tree DNA offer a range of single SNPs at US $39 per SNP. SNPs can only be ordered by existing FTDNA customers who have already taken a Y chromosome DNA test with the company. In October 2013 over 3500 individual SNPs were available to order from FTDNA. The placement on the phylogenetic tree is unknown for most of them. SNPs with a known placement are highlighted in the customer's personal results page under the Y-DNA Haplotree & SNPs section. Customers can also request that new SNPs are added to the catalogue.
YSEQ is a new company established by Thomas and Astrid Krahn in November 2013. YSEQ offer a potentially unlimited menu of single SNPs to order. For further details of this company see the blog post by Debbie Kennett entitled YSEQ a new company offering single SNPs.
Full Genomes Corporation have indicated that they will soon be offering single SNPs for sale.
Checking for similarity mainly to X and primer development using +/-500bp: up to 90% is good, up to 95% possible - http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
Deep clade tests
Family Tree DNA used the term "deep clade test" to refer to a panel of Y-chromosome SNP tests. This panel was intended to establish which particular subclade the Y-chromosome belonged to. The deep clade test was effectively superseded by the new Geno 2.0 test from the Genographic Project. This new test was introduced in the autumn/fall of 2012 and tests over 12,000 Y-DNA SNPs.
In January 2013 FTDNA announced that they were removing the deep clade test from sale. A link is now provided that will allow people to order the Genographic 2.0 test, whose Y-SNP results can be transferred back to Family Tree DNA.
Family Tree DNA announced at their conference in November 2013 that they would be reintroducing some deep clade tests in 2014, probably in the first quarter of the year.
Next generation sequencing
Next generation sequencing tests are the most advanced SNP tests available on the market and can be used for SNP discovery. There are currently two products available for the genetic genealogy market: the Big Y test from Family Tree DNA and the Y Elite 2.0 test from Full Genomes Corporation.
- The future of comprehensive Y testing is here by Kelly Wheaton. Lesson 15: Beginners' Guide to Genetic Genealogy.
- Why SNP testing is important by Robert Casey
- How To - Y-SNPs (Genealogical Viewpoint) by Robert Casey
- How To - Y-SNPs (Deep Ancestry Viewpoint) by Robert Casey
- How To - Y-SNPs (Future Trends) by Robert Casey
- The full Y-chromosome sequencing economic challenge A diagram prepared by Michael Walsh.
- Why SNP? Article published on the ISOGG website, 16 January 2008.
FTDNA Learning Center articles
- How to figure out what Y SNPs are tested at 23andme by Kitty Cooper, Kitty Cooper's blog, 23 February 2014.
- A confusion of SNPs by Debbie Kennett, Cruwys News blog, 15 November 2013.
- A simplified Y-tree and a common standard for Y-DNA haplogroup and SNP nomenclature by Debbie Kennett, Cruwys News blog, 8 November 2013.
- The changing names of Y-DNA by Judy Russell, The Legal Genealogist blog, 27 January 2013
- To SNP or not to SNP by Roberta Estes, DNAeXplained blog, 10 August 2012
"Y-SNPs - key to the future" - a presentation by Robert Casey explaining the importance of SNP testing:
- The price was raised from $29 per SNP to $39 per SNP in January 2013.
- "Exciting new developments at FTDNA". E-mail from Family Tree DNA to Y-DNA haplogroup project administrators, 25 January 2013.