The Genome that Won A Nobel Prize

My group met recently to discuss the in-press-at-Nature publication of Jim Watson’s genome – the first diploid human genome to be sequenced with next-generation technology. I’ve been waiting for this since 454 announced the project’s completion at the HGM2007 meeting last year in Montreal. It’s a landmark publication in terms of human genetic variation, and of particular interest to me since I work on our center’s 454 analysis pipeline.

In two months Roche/454 generated ~106.5 million genomic reads from Watson’s DNA in 234 runs. Using BLAT they mapped 93.2 million reads (87.5%) to hg36, yielding an average coverage of about 7.4x. No doubt the expense of this effort was substantial, though the authors claim it was 1/100^th of what capillary sequencing would have cost. It probably also hurt to throw away 2.5 million “unmapped” reads, though they did some post-processing of these with interesting results.

After a few filters were applied, the authors produced a set of 3.32 million SNPs in Watson’s genome, a number deliciously comparable to Craig Venter’s 3.47 million SNPs. In both men >80% of the SNPs are already known (to dbSNP). The most recent build of dbSNP (build 128), which doesn’t yet include novel Watson/Venter SNPs, has 9.89 million SNPs. The authors didn’t say but I estimate that the men share about 300,000 novel SNPs. Together they’ll add about 10% to the set of known SNPs, and only 1-2% of nonsynonymous SNPs. I hate to break it to you, but the sun is setting for nsSNPs. We know about 95% of them already and in Jim Watson only 7% are likely to be deleterious.

Also, over at GeneticFuture Daniel MacArthur discusses how the Watson Genome may be gloomy news for the field of personal genomics.  He points out that we’re perhaps five years away from affordable whole-genome sequencing, and by then we will no doubt have a much better understanding of how functional variation affects human phenotypes.

Indels are why I love 454 technology. In Watson’s genome they identified >200,000 indels of at least 2bp. Insertion detection is limited by read length, and so most were <200 bp. The largest deletion, however, was nearly 40 kbp. Only a fraction of the indels (~350) affected coding sequence. They saw a validation rate of 70% for a sampling of coding indels between 2 and 50 bp, which is pretty good. Single-base indels were treated with extreme caution, as over 80% of these were associated with homopolymers, the Achilles heel of 454 sequencing.

This paper was worth the wait. Not only was it an impressive demonstration of the power of 454 sequencing for whole-genome sequencing, but it openly addressed many of the informatics challenges therein and answered some interesting questions along the way. We can now confidently say that an individual carries ~3.7 million SNPs relative to the reference sequence, of which perhaps 10,000 are protein-altering. Ten of Watson’s nsSNPs were Mendelian-recessive, highly penetrant, disease-causing alleles according to HGMD, suggesting that each of us carries many more deleterious alleles than was previously believed. Yet analysis of the unplaced 454 reads suggests that as many as 100 protein-coding genes are still absent from the reference sequence. It seems like the work on the human genome is never done. I certainly know the feeling.

Still Waiting for that ABI SOLiD Genome

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.