Neandertal SNP Data
Letsinger, Ayland C
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Jairo Navarro Gonzalez
Hello Ayland,
Thank you for using the UCSC Genome Browser and your inquiry.
You may be interested in the S SNPs track for hg19 as it shows single nucleotide polymorphisms (SNPs) used in a genome-wide scan for signals of positive selection in the human lineage since divergence from the Neandertal lineage:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=ntSssSnps
The first six characters of an item name, i.e. AAA_AD:0D,1A, show the status of the allele (A, D or _ if not known) in six genomes: human reference, San, Yoruba, Han, Papuan, and French, in that order. These six characters are followed by a colon showing the number of derived alleles, and the number of ancestral alleles found in Neandertals.
For example, the following SNP labeled AAA_AD:0D,1A has the ancestral allele in the reference human genome and in all of the modern human genomes except Han and French. Among Neandertals, one instance of the ancestral allele was found, but no instances of the derived allele.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genomics Institute
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Jairo Navarro Gonzalez
Hello Ayland,
Thank you for using the UCSC Genome Browser and your follow-up question.
The S SNPs track does not necessarily include all known (at the time) SNPs for which Neandertal sequence was available and instead is a set of SNPs that were selected to be used for a genome-wide scan for signals of positive selection in the modern human lineage. The track description page has more to say about the SNPs that were selected, for example:
SNPs at CpG sites were excluded because of the higher mutation rate at CpG sites.
In addition to that, as you mention, coverage is probably an issue. Another possible issue is the sample size as there are very few Neandertals to sequence compared to the number of modern humans in dbSNP. One of our engineers suggests this may be why the authors of the Neandertal paper chose to use a handful of individual modern human genomes in their analysis. Also, the analysis used an older version of dbSNP (2010 or earlier), which has grown exponentially in the past few years (e.g., snp130 had 18.4 million items, compared to 234 million in snp150).
The publication mentioned in the References section of the track description page, A draft sequence of the Neandertal genome, might have more information as to why these SNPs were chosen in the analysis. If the publication doesn't describe how the S SNPs were selected out of all known-at-the-time SNPs, then you should try contacting the authors for more information.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Jairo Navarro
UCSC Genomics Institute
Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining
Jairo,You are a lifesaver! Thank you! Would you know the primary reason many SNPs do not have any Neandertal information? Is it just coverage, incomplete DNA, or simply differences in the genome?Ayland