{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,27]],"date-time":"2026-01-27T08:18:05Z","timestamp":1769501885753,"version":"3.49.0"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2020,4,21]],"date-time":"2020-04-21T00:00:00Z","timestamp":1587427200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004099","name":"Ligue Nationale Contre le Cancer","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100004099","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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; \u223c1X 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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>shallowHRD R script and documentation are available at https:\/\/github.com\/aeeckhou\/shallowHRD.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa261","type":"journal-article","created":{"date-parts":[[2020,4,14]],"date-time":"2020-04-14T19:14:52Z","timestamp":1586891692000},"page":"3888-3889","source":"Crossref","is-referenced-by-count":61,"title":["ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3574-9911","authenticated-orcid":false,"given":"Alexandre","family":"Eeckhoutte","sequence":"first","affiliation":[{"name":"DNA Repair and Uveal Melanoma (D.R.U.M.) , Inserm U830, Institut Curie, Paris 75248, France"},{"name":"Institut Curie , PSL Research University, Paris 75005, France"}]},{"given":"Alexandre","family":"Houy","sequence":"additional","affiliation":[{"name":"DNA Repair and Uveal Melanoma (D.R.U.M.) , Inserm U830, Institut Curie, Paris 75248, France"},{"name":"Institut Curie , PSL Research University, Paris 75005, France"}]},{"given":"Elodie","family":"Mani\u00e9","sequence":"additional","affiliation":[{"name":"DNA Repair and Uveal Melanoma (D.R.U.M.) , Inserm U830, Institut Curie, Paris 75248, France"},{"name":"Institut Curie , PSL Research University, Paris 75005, France"}]},{"given":"Manon","family":"Reverdy","sequence":"additional","affiliation":[{"name":"DNA Repair and Uveal Melanoma (D.R.U.M.) , Inserm U830, Institut Curie, Paris 75248, France"},{"name":"Institut Curie , PSL Research University, Paris 75005, France"}]},{"given":"Ivan","family":"Bi\u00e8che","sequence":"additional","affiliation":[{"name":"Department of Genetics , Institut Curie, Paris 75248, France"}]},{"given":"Elisabetta","family":"Marangoni","sequence":"additional","affiliation":[{"name":"Institut Curie , PSL Research University, Paris 75005, France"},{"name":"Department of Translational Research , Institut Curie PSL Research University, Paris 75248, France"}]},{"given":"Oumou","family":"Goundiam","sequence":"additional","affiliation":[{"name":"Institut Curie , PSL Research University, Paris 75005, France"},{"name":"Department of Translational Research , Institut Curie PSL Research University, Paris 75248, France"}]},{"given":"Anne","family":"Vincent-Salomon","sequence":"additional","affiliation":[{"name":"Department of Biopathology , Institut Curie PSL Research University, Paris 75005, France"}]},{"given":"Dominique","family":"Stoppa-Lyonnet","sequence":"additional","affiliation":[{"name":"DNA Repair and Uveal Melanoma (D.R.U.M.) , Inserm U830, Institut Curie, Paris 75248, France"},{"name":"Faculty of Medicine , University of Paris, Paris, France"}]},{"given":"Fran\u00e7ois-Cl\u00e9ment","family":"Bidard","sequence":"additional","affiliation":[{"name":"Department of Medical Oncology , Institut Curie PSL Research University, Paris 75248, France"},{"name":"Versailles Saint Quentin en Yvelines University , Paris Saclay University, Versailles 78035, France"}]},{"given":"Marc-Henri","family":"Stern","sequence":"additional","affiliation":[{"name":"DNA Repair and Uveal Melanoma (D.R.U.M.) , Inserm U830, Institut Curie, Paris 75248, France"},{"name":"Institut Curie , PSL Research University, Paris 75005, France"},{"name":"Department of Genetics , Institut Curie, Paris 75248, France"}]},{"given":"Tatiana","family":"Popova","sequence":"additional","affiliation":[{"name":"DNA Repair and Uveal Melanoma (D.R.U.M.) , Inserm U830, Institut Curie, Paris 75248, France"},{"name":"Institut Curie , PSL Research University, Paris 75005, France"}]}],"member":"286","published-online":{"date-parts":[[2020,4,21]]},"reference":[{"key":"2023063011294436700_btaa261-B1","doi-asserted-by":"crossref","first-page":"1776","DOI":"10.1038\/bjc.2012.451","article-title":"Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer","volume":"107","author":"Abkevich","year":"2012","journal-title":"Br. 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