ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing
Abstract
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.
Fichier principal
Eeckhoutte-2020-Shallowhrd-detection-of-homologous-.pdf (190.77 Ko)
Télécharger le fichier
Origin : Publication funded by an institution