Abstract 1280: Chromosome-scale haplotyping enables comprehensive discovery of cancer rearrangements and germline-related susceptibility mutations
Authors: Greer Stephanie U. , Lau Billy T. , Nadauld Lincoln D. , Ji Hanlee P. 
Published: August 2018

Abstract
To understand the complexity of cancer genomes, one needs to define both the structure and order of genomic variants relative to their respective parental chromosome. This process is commonly referred to as phasing and generates haplotypes with group of variants that originated from one parental chromosome or the other. Importantly, genetic variants such as rearrangements are difficult to detect and phase with conventional next-generation sequencing; short reads do not contain long-range genomic information for phasing. Recently, we demonstrated a new technology called linked-read sequencing, which uses droplet barcoding to tag high-molecular-weight (HMW) DNA in order to reconstruct genomic haplotypes and SVs in the range of megabases. Using single nanograms of DNA, we determined the structure of normal and cancer genomes at single-molecule resolution. In this study, we developed a method to generate haplotypes spanning entire chromosome arms and even across centromeric regions. The method is based on leveraging identity-by-descent (IBD) principles in haplotype-resolved sequence data. Taking advantage of shared haplotypes between an individual and a single parent, we exploited the fact that any single chromosomal homologue consists of a contiguous segment from one parent regardless of any recombination events that occurred during meiosis. By determining which of the two homologous segments in a haplotyped segment belongs to a parent, we can then stitch together the haplotypes that are physically contiguous in the child. Using phased haplotypes generated from linked-read sequencing, we improve on the experimentally generated haplotypes by at least an order of magnitude. As a control, we performed this type of analysis on a series of control genomes with comprehensive haplotype information. We achieved near-perfect concordance in the comprehensive phasing of these control samples regardless of which parental genome was used. We performed this analysis on linked-read whole-genome sequence data derived from familial cohorts with an inherited predisposition to cancer of unknown origin. For example, in one family predisposed to cholangiocarcinoma, we resolved the haplotype structure of entire chromosomes and segregated entire segments belonging to affected and unaffected individuals. A similar process was applied to the cancer samples originating from affected family members. The joint information was used to identify potential candidate driver genes for this cancer type. Overall, we demonstrated the utility of linked-read analysis and whole-chromosome haplotypes in discovering cancer genes.
Citation Format: Stephanie U. Greer, Billy T. Lau, Lincoln D. Nadauld, Hanlee P. Ji. Chromosome-scale haplotyping enables comprehensive discovery of cancer rearrangements and germline-related susceptibility mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1280.