David C. Wilkes

EXaCT-2 is a whole exome sequencing platform that detects various cancer-related genomic features with high accuracy and sensitivity, outperforming standard assays in detecting sub-clonal mutations and molecular metrics.

This paper introduces ppmSeq, a sequencing technology that improves accuracy and efficiency in detecting SNVs by sequencing both DNA strands, showing superior performance in clinical applications like ctDNA detection.

This study develops a pan-cancer PDO platform to preserve tumor heterogeneity and identify therapeutic vulnerabilities, finding that 58% of PDOs respond to Talazoparib and combination screens reveal resistance-overcoming drugs.

The paper analyzes whole-genome sequencing data from a pan-cancer cohort to define HRD, showing it extends beyond BRCA1/2 mutations and highlights the benefits of WGS over commercial assays for HRD detection.

This study examines how mutagenesis and extrachromosomal DNA contribute to urothelial cancer evolution, revealing clonal APOBEC3 mutations and chemotherapy-induced mutational bursts within ecDNA.

The paper identifies three novel complex structural variation patterns in cancer genomes using genome graph analysis across 2,833 tumor WGS.

Pore-C reads multi-way chromatin contacts directly off unamplified Nanopore long reads, recovering Hi-C-scale features while also resolving rearranged cancer alleles and supporting de novo assembly.