We’ve been fans of Evan Eichler’s since the earliest days of his work in segmental duplication and genome hotspots — so it’s great to see that he’s at it again. In this new Nature paper, Eichler and lead author Mark Chaisson at the University of Washington, along with collaborators from a number of institutions, use long-read PacBio sequencing to close or shrink 55 percent of the gaps remaining in the human reference genome.
The team used a hydatidiform mole cell line — an unusual haploid human cell — and sequenced it to 40x, using our BluePippin to size select 20 Kb and 30 Kb libraries. The genomic regions they addressed most frequently were ones that have proven challenging for other kinds of sequencers: GC-rich sequences and complex structural variants. The authors present a number of never-previously-reported variants: 85 percent of the copy number variants they detected; 92 percent of insertions; and 69 percent of deletions they spotted. Through this great effort, the team added more than a megabase of novel sequence to the human genome.
To learn more, check out the paper: Resolving the complexity of the human genome using single-molecule sequencing. It offers a fascinating view of the complexity in the human genome, much of which has never been seen before.