US EPA

7323308 

Journal Article 

ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing 

Eeckhoutte, A; Houy, A; Manié, E; Reverdy, M; Bièche, I; Marangoni, E; Goundiam, O; Vincent-Salomon, A; Stoppa-Lyonnet, D; Bidard, FC; Stern, MH; Popova, T 

2020 

36 

12 

3888-3889 

English 

32315385 

10.1093/bioinformatics/btaa261 

WOS:000550127500039 

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.