Breast Cancer Structural Variant Features Unearthed With Long-Read Sequencing

In a paper appearing in the European Journal of Human Genetics, a team from the University of British Columbia, Canada's Michael Smith Genome Sciences Centre, and BC Cancer share findings from a long-read sequencing-based analysis of risky germline structural variants (SVs) falling in breast cancer susceptibility genes — an approach that made it possible to pick up SV breakpoints, highlighting allelic heterogeneity within the genes considered. With the help of nanopore long-read sequencing, the researchers sequenced the genomes of 19 individuals carry alterations affecting four well-known breast cancer-related genes: BRCA1/2, PALB2, or CHEK2. In the process, they identified 14 copy number variants (CNVs) in moderate- or high-penetrance genes, which were explored more fully with structural variant breakpoint profiling made possible by the long-read sequences. The authors reason that long-read sequencing can reveal "cryptic, copy neutral, and complex rearrangements whose clinical or functional significance is uncertain," adding that such variants "remain undetected or unresolved by [short-read sequencing], suggesting their contribution to cancer susceptibility may be underappreciated."