Tuesday, November 25, 2008

L24 (rs35248080) Background Information

The Y-DNA J-L24 clade is defined by a SNP in haplogroup J2 called L24 by FTDNA and rs35248080 by the scientific community in general. This is a very new SNP so the population geneticists and genetic genealogists will, in the near future, provide additional names for this SNP and clade. L24 (rs35248080) was first reported by Perlegen in August 2005 and additional information can be found at the dbSNP website by searching for rs35248080. Unfortunately this SNP has not been previously researched widely so there is currently no useful statistical information available. We do know that rs35248080 (L24) is located at position 12796528 on the Y-chromosome and that the ancestral state for this SNP is G and the derived (mutated) state is A. In addition we know that rs35248080 (L24) is located at an intergenic region of the Y-chromosome. That is, it is not located within a Y-chromosome gene so that there are no specific medical features that can be attributed to the L24 mutation.

In 2007 significant progress was made in the SNP array technology where hundreds of thousands of SNPs could be detected within an organism in a single test. See the Microarrays primer at NCBI (National Center for Biotechnology Information) for further information. Our incredible good fortune was that two companies, Affymetrix and Illumina , included rs35248080 (L24) in their SNP arrays. These two companies are indicated as including rs35248080 in the NCBI Assay ID at the dbSNP website. It was also good fortune that in late 2007, three companies, 23andMe , deCODEme, and Navigenics announced genome-wide tests using the new SNP array technology from Affymetrix and Illumina. Now thousands of SNPs could be tested in the autosomes, X & Y chromosomes, and the mitochondrial DNA. Of particular interest to genetic genealogists were the numerous new SNPs being tested in the Y-chromosome which they saw as a wonderful opportunity to enhance knowledge of the Y-chromosome phylogenetic tree. The genetic genealogists, commencing in mid to late 2008, on the GENEALOGY-DNA and DNA-FORUMS list tested themselves, organized funding campaigns, and encouraged others to test with deCODEme and 23andMe. The volunteers downloaded their raw Y-chromosome results from deCODEme and 23andMe and sent them to Dr. Ann Turner and Adriano Squecco who compiled the data on Excel spreadsheets for everyone on these public forums to view, discuss, and analyze. Adriano Squecco also programmed in Excel so that one could easily see where the derived (mutated) SNP states were located. Adriano continues collecting data and his zipped Microsoft Excel spreadsheet can be found here. If you do not have Microsoft Excel then an excellent alternative is the Calc program found in the public domain (free) OpenOffice suite.

One of the first Y-DNA haplogroup J people to test with deCODEme was Walter Krol and it was Adriano Squecco who on 19 Sep 2008 announced rs35248080 (L24) in Krol's results. We knew then that we had a new Y-SNP, a new clade, in J2a. Adriano also detected rs34126399 (now known as L27 by FTDNA) in Krol's sample. However, rs34126399 was previously described by Dr. Roy King on 25 Jul 2008 in 23andMe's SPITTOON blog. Both Dr. King and Dr. Peter Underhill, geneticists at Stanford University, are consultants for 23andMe. Dr. Underhill's group at Stanford University has discovered many Y-SNPs, the M series of SNPs.

These results were very exciting to those of us who have waited so long to see further definition in the J2 phylogenetic tree. I wanted to test with 23andMe early on, but the price tag (~1000$) was just too much for me. However, in Sep 2008, 23andMe announced that they had increased the number of SNPs tested in the Y-chromosome by approximately 1000 (!) and in addition they had lowered the price for their test to ~$400. I could hold back no longer! 23andMe received my sample on 26 Sep 2008 and my results were available on 15 Oct 2008. It was a pleasure to confirm rs35248080(L24) and rs34126399 (L27) in my own sample. In addition I found two other SNPs that did not show up in Krol's deCODEme results. They were rs34534058 (L25), and rs34459399 (L26). Further tests by Dr. Thomas Krahn at FTDNA confirmed that L26 is equivalent to L27, and that L25 is equivalent to L24. L26/L27 are just "downstream" from the J2a defining SNP called M410. L24/L25 define a new subclade of J2a downstream from L26/L27. These new SNPs are causing a re-ordering of the Y-chromosome tree below J2a-M410. Things are in a state of flux right now but a nice working draft of the new J-tree is available at Dr. Krahn's DNA-Fingerprint website. I also found 3 new J SNPs in my results equivalent apparently to the J-M304 SNP. These are: rs17306965, rs17307175, and rs34987551. Bonnie Shrack found two other J-SNPs in my results too, also apparently equivalent to J-M304, and they are: rs17316547 and rs17250845.

Walter Krol, helping as much as possible, also tested with 23andMe. He confirmed the L25 and L26 derived states that I had. Also Adriano Squecco found two additional SNPs that Krol tested positive for (was derived for). These were rs17306699 and rs34986875. The SNP rs17306699 with the G state is known as P129 and it is a haplogroup IJ SNP. Krol had the A state for this SNP, the ancestral state. He had a "back mutation" at rs17306699. So while Krol has the same SNPs as I do in L24/L25 and L26/L27 he defines a new subclade of L24/L25, distinct from me as I carry the G state for rs17306699. This result, however, needs to be confirmed. Also Andriano found that Krol was derived for rs34986875 with the C state (the ancestral state is T). Unfortunately I had a no-call for this SNP (no result!) so it is not known at this time if we both carry the same state or we are different again! We can only wait for other J2a's to test with 23andMe to find out. New results should be coming in soon.

Hopefully soon we will see FTDNA offering these new J-SNPs for testing (L24-L27 at least). Also, and finally for now, I want to mention another website for learning about SNPs: SNPedia. In addition I need to mention that the International Society of Genetic Genealogists (ISOGG) maintains a Y-DNA tree found here. Their J tree is found here. In this blog we will use SNP names such as M172 or L24 rather than clade/subclade names. The reason is that the SNP names are usually simple and unchanging over time and across laboratories.
UPDATED: 07 Feb 2009

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