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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.
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https://www.hal.inserm.fr/inserm-03034570
Contributor : Marc-Henri Stern <>
Submitted on : Tuesday, December 1, 2020 - 6:20:04 PM
Last modification on : Thursday, December 3, 2020 - 3:30:30 AM
Long-term archiving on: : Tuesday, March 2, 2021 - 8:15:35 PM

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Alexandre Eeckhoutte, Alexandre Houy, Elodie Manié, Manon Reverdy, Ivan Bièche, et al.. ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing. Bioinformatics, Oxford University Press (OUP), 2020, 36 (12), pp.3888-3889. ⟨10.1093/bioinformatics/btaa261⟩. ⟨inserm-03034570⟩

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