Application and use of long-read sequencing in personalized cancer medicine

Abstract

In this study we sought to understand what additional information could be gleaned from long-read sequencing using the Oxford Nanopore Technologies PromethION platform. This analysis was done on a cohort of patients from a larger prospective study from British Columbia, Canada, called the Personalized Oncogenomics (POG) Program, in which patients with advanced cancers provide a sample for whole-genome transcriptome sequencing and analysis. The long-read POG dataset comprises a sub-cohort of 189 patient tumours and 41 matched normal samples who have both the long-read and standard “short” read sequencing. This data set has demonstrated the potential of long-read sequencing for resolving complex cancer-related structural variants, viral integrations, and extrachromosomal circular DNA. From a clinical perspective we have used this data to explain the presence of homologous recombination deficiency (HRD) due to promoter methylation in *BRCA1 *and *RAD51C *where no driver mutation could be identified.

Biography

Dr. Laskin is a Clinical Associate Professor in the Department of Medicine at The University of British Columbia, Canada. She is also an Associate Member in Canada’s Michael Smith Genome Sciences Centre, and a Medical Oncologist at BC Cancer, in Vancouver. Dr. Laskin’s research is focused on genomic and personalized medicine as the clinical program leader for the Personalized Oncogenomics (POG) Program. POG is a collaborative translational research effort that uses in-depth genomic sequencing to guide chemotherapy decision-making in a clinically relevant timeframe.