NCM 2023 Singapore: The 1000 Genomes Project Oxford Nanopore Sequencing Consortium: expanding our understanding of human genetic variation

Growing evidence demonstrates that structural variants (SVs; insertions, deletions, duplications, repeat expansions, and translocations >50 bp) make significant contributions to genetic diversity and disease susceptibility. Identification and complete characterization of SVs is challenging using short-read-sequencing-based approaches, which detect only half of the ~25,000 SVs present in an individual and are incapable of fully resolving the complex structure of many SVs. These challenges extend into the clinical testing space where commonly used approaches, such as exome sequencing, have low sensitivity for SV detection, meaning individuals with disease-causing SVs may remain undiagnosed after comprehensive testing. Thus, there is broad interest in using new technologies such as long-read sequencing (LRS) to develop more comprehensive catalogues of normal human SV patterns to better identify disease-causing SVs in undiagnosed individuals. The 1000 Genomes Oxford Nanopore Technologies Sequencing Consortium is an international effort to sequence at least 800 of the 1000 Genomes Project Samples on the Oxford Nanopore Platform to identify SVs missed by prior short-read-based approaches, evaluate variants in difficult-to-analyse regions of the genome, and evaluate both assembly and alignment-based approaches to LRS data analysis. Preliminary results from analysis of 100 individuals sequenced as part of this effort will be presented (average depth of coverage, 30x; read N50, 50 kb). Because a major goal of this effort is to develop a catalogue of common human SVs for filtering and prioritizing disease-associated SVs, results from filtering variants in unsolved cases to identify high-priority regions for later analysis will be shown.

Authors: Danny E. Miller