Dataset Information
ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing.
Ontology highlight
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.
SUBMITTER: Eeckhoutte A
PROVIDER: S-EPMC7320600 | biostudies-literature | 2020 Jun
REPOSITORIES: biostudies-literature
Publications
ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing.
Bioinformatics (Oxford, England) 20200601 12
<h4>Summary</h4>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 tu ...[more]
