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At ASHG, Francis Collins Reports on Sequencing, Haplotypes, and More

TORONTO, Oct. 28 (GenomeWeb News) - During a break in sessions here at the 54th annual American Society of Human Genetics meeting yesterday, National Human Genome Research Institute leader Francis Collins sat down with a handful of reporters to discuss progress and future plans of the institute. This briefing ties into the report of the same theme that Collins' team delivers each year to the ASHG board.

 

Foremost on Collins' mind was the landmark, albeit anticlimactic,  publication in last week's Nature reporting the finished human genome sequence. With just 341 remaining gaps that cannot be closed with modern technology, Collins called the final work "very gratifying," noting that its error rate is 1 out of every 100,000 base pairs - an accuracy higher than originally targeted by the sequencing consortium.

 

Collins also pointed out that subsequent studies of the genome sequence have proven that that level of accuracy could not have been reached with a pure shotgun-based approach. To correctly identify the segmented regions - more than 5 percent of the genome - scientists needed to perform the more painstaking and time-consuming clone-by-clone method, he said.

 

The community hasn't seen the last of human genome-sequence publications, though. Researchers' reports on some of the individual chromosomes are still in the works; Collins expected the remainder to be published in the next six to eight months.

 

In other sequencing updates, Collins mentioned the 18 new organisms recently approved for the pipelines at the major production centers. Most were chosen in part based on evolutionary branch length between organisms, he said. "This seems like a very good investment of the sequencing pipeline we've got," he said. After that load is through the pipeline, which he said could come as early as next summer, he expects to see more teams pushing to sequence additional primate genomes.

 

In another topic that has been getting a fair amount of attention at this conference, Collins addressed the HapMap program's progress in genotyping populations across three major geographic areas. Early work, he said, indicates that 85 percent to 90 percent of human variation occurs within a population, with the rest occurring between populations.

 

Whether such genomic data supports the idea of distinct human races has become a hot topic at ASHG this year, and discussions of the issue seem to have some people on tenterhooks. "Maybe we need to throw out the term 'race' because it has so much baggage," said Collins, who contended that markers found to distinguish between populations indicate "ancestral geographic regions" rather than the more cultural concept of race.

 

Collins also spoke with gathered reporters about the idea of a large-scale cohort study in the USakin to what the UKhas done with Biobank. Such a project would entail studying "very large numbers of people over a long period of time," he said. "That would be a major undertaking along the lines of the genome project" in terms of cost and time commitment, he added. While he's hopeful that it could one day get off the ground, simply proposing the concept is a dead end without a bill barring genetic discrimination - as it is today, people have considerable incentive not to participate in such a study, he said.

 

A bill that would've done this stalled in Congress this year, but Collins said he hopes to see it reintroduced next year. "At the moment," he said, a large cohort study in the USis "purely a scientific discussion." To that end, a group at NHGRI has been "working on this intensely for the past six months" to determine basic feasibility and logistical issues such as how many people would be needed, he said. Those efforts could result in a white paper as early as next spring.

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