ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing
Alexandre Eeckhoutte, Alexandre Houy, Élodie Manié, Manon Reverdy, Ivan Bièche, Elisabetta Marangoni, Oumou Goundiam, Anne Vincent‐Salomon, Dominique Stoppa‐Lyonnet, François‐Clément Bidard, Marc‐Henri Stern, Tatiana Popova
Abstract
SUMMARY: We introduce shallowHRD, a software tool to evaluate tumor homologous recombination deficiency (HRD) based on whole genome sequencing (WGS) at low coverage (shallow WGS or sWGS; ∼1X coverage). The tool, based on mining copy number alterations profile, implements a fast and straightforward procedure that shows 87.5% sensitivity and 90.5% specificity for HRD detection. shallowHRD could be instrumental in predicting response to poly(ADP-ribose) polymerase inhibitors, to which HRD tumors are selectively sensitive. shallowHRD displays efficiency comparable to most state-of-art approaches, is cost-effective, generates low-storable outputs and is also suitable for fixed-formalin paraffin embedded tissues. AVAILABILITY AND IMPLEMENTATION: shallowHRD R script and documentation are available at https://github.com/aeeckhou/shallowHRD. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.