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

被引：47

作者：

Eeckhoutte, Alexandre ^{[1
,2
]}

Houy, Alexandre ^{[1
,2
]}

Manie, Elodie ^{[1
,2
]}

Reverdy, Manon ^{[1
,2
]}

Bieche, Ivan ^{[3
]}

Marangoni, Elisabetta ^{[2
,4
]}

Goundiam, Oumou ^{[2
,4
]}

Vincent-Salomon, Anne ^{[5
]}

Stoppa-Lyonnet, Dominique ^{[1
,6
]}

Bidard, Francois-Clement ^{[7
,8
]}

Stern, Marc-Henri ^{[1
,2
,3
]}

Popova, Tatiana ^{[1
,2
]}

机构：

[1] Inst Curie, IDNA Repair & Uveal Melanoma DRUM, INSERM, U830, F-75248 Paris, France

[2] PSL Res Univ, Inst Curie, F-75005 Paris, France

[3] Inst Curie, Dept Genet, F-75248 Paris, France

[4] PSL Res Univ, Dept Translat Res, Inst Curie, F-75248 Paris, France

[5] PSL Res Univ, Dept Biopathol, Inst Curie, F-75005 Paris, France

[6] Univ Paris, Fac Med, Paris, France

[7] PSL Res Univ, Dept Med Oncol, Inst Curie, F-75248 Paris, France

[8] Univ Paris Saclay, Versailles St Quentin Yvelines Univ, F-78035 Versailles, France

来源：

BIOINFORMATICS | 2020年 / 36卷 / 12期

关键词：

COPY-NUMBER; REPAIR; REVEALS;

D O I：

10.1093/bioinformatics/btaa261

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

aSummary: 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; similar to 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.

引用

页码：3888 / 3889

页数：2

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