Vikas Bansal, Ph.D.
University of California, San Diego
School of Medicine
Dept. of Pediatrics
Lab Website
“Haplotype-resolved whole-genome sequencing using short reads and long reads”
Thursday, Nov. 8, 2018
2 PM
RRI 101
Abstract: Humans are diploid and long-range haplotype information is crucial for genetic mapping in Mendelian and complex disorders, population genetics analyses, and for the complete interpretation of variants in individual genomes. However, the short read lengths of sequencing technologies such as Illumina limit the ability to reconstruct haplotypes for individual genomes. We have previously developed state-of-the-art computational tools for haplotype assembly from sequence data. We have also demonstrated that chromosomal-spanning haplotypes for human genomes can be assembled using our haplotype assembly tool, HapCUT, applied to proximity-ligation (HiC) sequence data. Recently, we have developed a computational method that enables haplotype-resolved variant detection directly from error-prone long reads generated using the Pacific Biosciences SMRT technology. This method has high precision and recall for single nucleotide variants (0.994 and 0.974 respectively), significantly better than existing variant calling methods, and can enable variant calling in segmental duplications with high sequence identity that are inaccessible to short reads. We are also working to enable accurate and complete haplotyping using short read Illumina sequencing. Using data from four human genomes sequenced using a novel HiC protocol, we have assembled highly accurate whole-genome haplotypes. Our results demonstrate that haplotype-resolved whole-genome sequencing is feasible using both long and short read technologies and likely to become routine in the near future.
Host: Mark Chaisson
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