Jasmine: Population-scale structural variant comparison and analysis

Kirsche, Melanie, Prabhu, Gautam, Sherman, Rachel, Ni, Bohan, Aganezov, Sergey, Schatz, Michael (May 2021) Jasmine: Population-scale structural variant comparison and analysis. BioRxiv. (Unpublished)

PDF 2021.Kirsche.structural_variant_comparison.pdf Available under License Creative Commons Attribution. Download (2MB)

Abstract

The increasing availability of long-reads is revolutionizing studies of structural variants (SVs). However, because SVs vary across individuals and are discovered through imprecise read technologies and methods, they can be difficult to compare. Addressing this, we present Jasmine (https://github.com/mkirsche/Jasmine ), a fast and accurate method for SV refinement, comparison, and population analysis. Using an SV proximity graph, Jasmine outperforms five widely-used comparison methods, including reducing the rate of Mendelian discordance in trio datasets by more than five-fold, and reveals a set of high confidence de novo SVs confirmed by multiple long-read technologies. We also present a harmonized callset of 205,192 SVs from 31 samples of diverse ancestry sequenced with long reads. We genotype these SVs in 444 short read samples from the 1000 Genomes Project with both DNA and RNA sequencing data and assess their widespread impact on gene expression, including within several medically relevant genes.

Item Type:	Paper
Subjects:	bioinformatics > computational biology Investigative techniques and equipment > assays > long-read sequencing structural biology
CSHL Authors:	Schatz, Michael C.
Communities:	CSHL labs > Schatz lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	28 May 2021
Date Deposited:	02 Jun 2021 13:50
Last Modified:	02 Jun 2021 13:50
URI:	https://repository.cshl.edu/id/eprint/40187

Actions (login required)

Administrator's edit/view item