Kortine Kleinheinz

The paper introduces a framework for assessing the quality of whole genome cancer sequences using a star rating system based on five QC measures, providing a tool for researchers to evaluate and exclude low-quality data.

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

ACEseq estimates allele-specific copy numbers, tumor purity, ploidy, and homologous recombination deficiency scores from tumor whole-genome sequencing by combining GC-bias correction, replication-timing correction, and structural variant breakpoints.

The paper describes the PCAWG project's large-scale analysis of cancer whole genomes across multiple computing environments, producing validated consensus variants for downstream research.