One of the big announcements at this year’s AGBT was ABI’s sequencing of a complete human genome using the SOLiD system. It wasn’t just any genome, either – it was the genome of an African male of the Yoruba tribe in Nigeria (one of the HapMap samples). Perhaps I should be unsurprised that the press releases flew months ago but we’ve yet to see the peer-reviewed publication. Yet I’m eager to read the results of their project, as it will be the first complete genome sequencing of an individual from the African continent. Many studies have seen higher incidence and allele frequencies of SNPs in African samples, consistent with population bottlenecks during out-of-Africa expansions. In fact, a recent genome-wide survey of genetic variation in 51 populations showed that humans formed a chain of colonies as they migrated out of Africa some 10,000 years ago. That article’s a very interesting read.
But back to ABI. Perusing the SOLiD web site, I did find a poster on the genome-wide variation detected from their not-yet-completed SOLiD sequencing. From it I took these key pieces of information. They sequenced both fragment and mate-pair libraries to a coverage of about 4.9X. The mate-pair libraries allowed them to detect ~22,000 insertions and ~45,000 deletions, nearly all of which were heterozygous. At ~4X coverage on chromosome 7, some 75% of the SNPs detected were already in dbSNP. In the ENCODE regions (which have been extensively characterized), 91% of the SNPs detected were in dbSNP. To me, the fraction of novel SNPs seems low, but if it remains constant, this study will almost certainly add more SNPs to public databases than the Watson and Venter efforts.