{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,9]],"date-time":"2026-11-09T21:11:49Z","timestamp":1794258709786,"version":"4.9.0"},"reference-count":51,"publisher":"Springer Science and Business Media LLC","issue":"4","license":[{"start":{"date-parts":[[2017,3,13]],"date-time":"2017-03-13T00:00:00Z","timestamp":1489363200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Med"],"published-print":{"date-parts":[[2017,4]]},"DOI":"10.1038\/nm.4292","type":"journal-article","created":{"date-parts":[[2017,3,13]],"date-time":"2017-03-13T12:08:17Z","timestamp":1489406897000},"page":"517-525","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1029,"title":["HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures"],"prefix":"10.1038","volume":"23","author":[{"given":"Helen","family":"Davies","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominik","family":"Glodzik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandro","family":"Morganella","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lucy R","family":"Yates","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johan","family":"Staaf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueqing","family":"Zou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manasa","family":"Ramakrishna","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sancha","family":"Martin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandrine","family":"Boyault","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1341-5400","authenticated-orcid":false,"given":"Anieta M","family":"Sieuwerts","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter T","family":"Simpson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tari A","family":"King","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5634-1539","authenticated-orcid":false,"given":"Keiran","family":"Raine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorunn E","family":"Eyfjord","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gu","family":"Kong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c5ke","family":"Borg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ewan","family":"Birney","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hendrik G","family":"Stunnenberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marc J","family":"van de Vijver","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne-Lise","family":"B\u00f8rresen-Dale","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3428-3366","authenticated-orcid":false,"given":"John W M","family":"Martens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul N","family":"Span","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sunil R","family":"Lakhani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne","family":"Vincent-Salomon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christos","family":"Sotiriou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8715-2901","authenticated-orcid":false,"given":"Andrew","family":"Tutt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alastair M","family":"Thompson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven","family":"Van Laere","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea L","family":"Richardson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alain","family":"Viari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter J","family":"Campbell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R","family":"Stratton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Serena","family":"Nik-Zainal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2017,3,13]]},"reference":[{"key":"BFnm4292_CR1","doi-asserted-by":"crossref","unstructured":"Anglian Breast Cancer Study Group. Prevalence and penetrance of BRCA1 and BRCA2 mutations in a population-based series of breast cancer cases. Br. J. Cancer 83, 1301\u20131308 (2000).","DOI":"10.1054\/bjoc.2000.1407"},{"key":"BFnm4292_CR2","doi-asserted-by":"publisher","first-page":"2869","DOI":"10.1001\/jama.298.24.2869","volume":"298","author":"EM John","year":"2007","unstructured":"John, E.M. et al. Prevalence of pathogenic BRCA1 mutation carriers in 5 US racial\/ethnic groups. J. Am. Med. Assoc. 298, 2869\u20132876 (2007).","journal-title":"J. Am. Med. Assoc."},{"key":"BFnm4292_CR3","doi-asserted-by":"publisher","first-page":"8297","DOI":"10.1158\/0008-5472.CAN-06-0503","volume":"66","author":"KE Malone","year":"2006","unstructured":"Malone, K.E. et al. Prevalence and predictors of BRCA1 and BRCA2 mutations in a population-based study of breast cancer in white and black American women ages 35 to 64 years. Cancer Res. 66, 8297\u20138308 (2006).","journal-title":"Cancer Res."},{"key":"BFnm4292_CR4","doi-asserted-by":"publisher","first-page":"1466","DOI":"10.1126\/science.1251827","volume":"343","author":"FJ Couch","year":"2014","unstructured":"Couch, F.J., Nathanson, K.L. & Offit, K. Two decades after BRCA: setting paradigms in personalized cancer care and prevention. Science 343, 1466\u20131470 (2014).","journal-title":"Science"},{"key":"BFnm4292_CR5","doi-asserted-by":"publisher","first-page":"1462","DOI":"10.1126\/science.1251900","volume":"343","author":"MC King","year":"2014","unstructured":"King, M.C. \u201cThe race\u201d to clone BRCA1. Science 343, 1462\u20131465 (2014).","journal-title":"Science"},{"key":"BFnm4292_CR6","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1038\/nature10760","volume":"481","author":"CJ Lord","year":"2012","unstructured":"Lord, C.J. & Ashworth, A. The DNA damage response and cancer therapy. Nature 481, 287\u2013294 (2012).","journal-title":"Nature"},{"key":"BFnm4292_CR7","doi-asserted-by":"publisher","first-page":"1470","DOI":"10.1126\/science.1252230","volume":"343","author":"AR Venkitaraman","year":"2014","unstructured":"Venkitaraman, A.R. Cancer suppression by the chromosome custodians, BRCA1 and BRCA2. Science 343, 1470\u20131475 (2014).","journal-title":"Science"},{"key":"BFnm4292_CR8","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1038\/nature03445","volume":"434","author":"H Farmer","year":"2005","unstructured":"Farmer, H. et al. Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature 434, 917\u2013921 (2005).","journal-title":"Nature"},{"key":"BFnm4292_CR9","doi-asserted-by":"publisher","first-page":"a016600","DOI":"10.1101\/cshperspect.a016600","volume":"7","author":"R Prakash","year":"2015","unstructured":"Prakash, R., Zhang, Y., Feng, W. & Jasin, M. Homologous recombination and human health: the roles of BRCA1, BRCA2, and associated proteins. Cold Spring Harb. Perspect. Biol. 7, a016600 (2015).","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"BFnm4292_CR10","doi-asserted-by":"publisher","first-page":"913","DOI":"10.1038\/nature03443","volume":"434","author":"HE Bryant","year":"2005","unstructured":"Bryant, H.E. et al. Specific killing of BRCA2-deficient tumours with inhibitors of poly(ADP-ribose) polymerase. Nature 434, 913\u2013917 (2005).","journal-title":"Nature"},{"key":"BFnm4292_CR11","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1056\/NEJMoa0900212","volume":"361","author":"PC Fong","year":"2009","unstructured":"Fong, P.C. et al. Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N. Engl. J. Med. 361, 123\u2013134 (2009).","journal-title":"N. Engl. J. Med."},{"key":"BFnm4292_CR12","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/S0140-6736(10)60893-8","volume":"376","author":"MW Audeh","year":"2010","unstructured":"Audeh, M.W. et al. Oral poly(ADP-ribose) polymerase inhibitor olaparib in patients with BRCA1 or BRCA2 mutations and recurrent ovarian cancer: a proof-of-concept trial. Lancet 376, 245\u2013251 (2010).","journal-title":"Lancet"},{"key":"BFnm4292_CR13","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1016\/S0140-6736(10)60892-6","volume":"376","author":"A Tutt","year":"2010","unstructured":"Tutt, A. et al. Oral poly(ADP-ribose) polymerase inhibitor olaparib in patients with BRCA1 or BRCA2 mutations and advanced breast cancer: a proof-of-concept trial. Lancet 376, 235\u2013244 (2010).","journal-title":"Lancet"},{"key":"BFnm4292_CR14","doi-asserted-by":"publisher","first-page":"1697","DOI":"10.1056\/NEJMoa1506859","volume":"373","author":"J Mateo","year":"2015","unstructured":"Mateo, J. et al. DNA-repair defects and olaparib in metastatic prostate cancer. N. Engl. J. Med. 373, 1697\u20131708 (2015).","journal-title":"N. Engl. J. Med."},{"key":"BFnm4292_CR15","doi-asserted-by":"publisher","first-page":"1382","DOI":"10.1056\/NEJMoa1105535","volume":"366","author":"J Ledermann","year":"2012","unstructured":"Ledermann, J. et al. Olaparib maintenance therapy in platinum-sensitive relapsed ovarian cancer. N. Engl. J. Med. 366, 1382\u20131392 (2012).","journal-title":"N. Engl. J. Med."},{"key":"BFnm4292_CR16","doi-asserted-by":"publisher","first-page":"R107","DOI":"10.1186\/bcr3049","volume":"13","author":"EH Lips","year":"2011","unstructured":"Lips, E.H. et al. Quantitative copy number analysis by Multiplex Ligation\u2013dependent Probe Amplification (MLPA) of BRCA1-associated breast cancer regions identifies BRCAness. Breast Cancer Res. 13, R107 (2011).","journal-title":"Breast Cancer Res."},{"key":"BFnm4292_CR17","doi-asserted-by":"publisher","first-page":"2090","DOI":"10.1016\/j.ejca.2014.05.001","volume":"50","author":"I Ruscito","year":"2014","unstructured":"Ruscito, I. et al. BRCA1 gene promoter methylation status in high-grade serous ovarian cancer patients\u2014a study of the Tumour Bank Ovarian Cancer (TOC) and Ovarian Cancer Diagnosis consortium (OVCAD). Eur. J. Cancer 50, 2090\u20132098 (2014).","journal-title":"Eur. J. Cancer"},{"key":"BFnm4292_CR18","doi-asserted-by":"publisher","first-page":"990","DOI":"10.1093\/jnci\/94.13.990","volume":"94","author":"AA Jazaeri","year":"2002","unstructured":"Jazaeri, A.A. et al. Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers. J. Natl. Cancer Inst. 94, 990\u20131000 (2002).","journal-title":"J. Natl. Cancer Inst."},{"key":"BFnm4292_CR19","doi-asserted-by":"publisher","first-page":"e64268","DOI":"10.1371\/journal.pone.0064268","volume":"8","author":"MJ Larsen","year":"2013","unstructured":"Larsen, M.J. et al. Classifications within molecular subtypes enables identification of BRCA1\/BRCA2 mutation carriers by RNA tumor profiling. PLoS One 8, e64268 (2013).","journal-title":"PLoS One"},{"key":"BFnm4292_CR20","doi-asserted-by":"publisher","first-page":"3361","DOI":"10.1038\/ncomms4361","volume":"5","author":"G Peng","year":"2014","unstructured":"Peng, G. et al. Genome-wide transcriptome profiling of homologous recombination DNA repair. Nat. Commun. 5, 3361 (2014).","journal-title":"Nat. Commun."},{"key":"BFnm4292_CR21","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1007\/s10549-008-0117-z","volume":"116","author":"SA Joosse","year":"2009","unstructured":"Joosse, S.A. et al. Prediction of BRCA1-association in hereditary non-BRCA1\/2 breast carcinomas with array-CGH. Breast Cancer Res. Treat. 116, 479\u2013489 (2009).","journal-title":"Breast Cancer Res. Treat."},{"key":"BFnm4292_CR22","doi-asserted-by":"publisher","first-page":"1561","DOI":"10.1093\/annonc\/mdq624","volume":"22","author":"MA Vollebergh","year":"2011","unstructured":"Vollebergh, M.A. et al. An aCGH classifier derived from BRCA1-mutated breast cancer and benefit of high-dose platinum-based chemotherapy in HER2-negative breast cancer patients. Ann. Oncol. 22, 1561\u20131570 (2011).","journal-title":"Ann. Oncol."},{"key":"BFnm4292_CR23","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1186\/bcr3670","volume":"16","author":"JA Watkins","year":"2014","unstructured":"Watkins, J.A., Irshad, S., Grigoriadis, A. & Tutt, A.N. Genomic scars as biomarkers of homologous recombination deficiency and drug response in breast and ovarian cancers. Breast Cancer Res. 16, 211 (2014).","journal-title":"Breast Cancer Res."},{"key":"BFnm4292_CR24","doi-asserted-by":"publisher","first-page":"6159","DOI":"10.1158\/1078-0432.CCR-10-1027","volume":"16","author":"M Graeser","year":"2010","unstructured":"Graeser, M. et al. A marker of homologous recombination predicts pathologic complete response to neoadjuvant chemotherapy in primary breast cancer. Clin. Cancer Res. 16, 6159\u20136168 (2010).","journal-title":"Clin. Cancer Res."},{"key":"BFnm4292_CR25","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1038\/nrc.2015.21","volume":"16","author":"CJ Lord","year":"2016","unstructured":"Lord, C.J. & Ashworth, A. BRCAness revisited. Nat. Rev. Cancer 16, 110\u2013120 (2016).","journal-title":"Nat. Rev. Cancer"},{"key":"BFnm4292_CR26","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1038\/nature07517","volume":"456","author":"DR Bentley","year":"2008","unstructured":"Bentley, D.R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53\u201359 (2008).","journal-title":"Nature"},{"key":"BFnm4292_CR27","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1038\/nature17676","volume":"534","author":"S Nik-Zainal","year":"2016","unstructured":"Nik-Zainal, S. et al. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 534, 47\u201354 (2016).","journal-title":"Nature"},{"key":"BFnm4292_CR28","doi-asserted-by":"publisher","first-page":"11383","DOI":"10.1038\/ncomms11383","volume":"7","author":"S Morganella","year":"2016","unstructured":"Morganella, S. et al. The topography of mutational processes in breast cancer genomes. Nat. Commun. 7, 11383 (2016).","journal-title":"Nat. Commun."},{"key":"BFnm4292_CR29","doi-asserted-by":"publisher","first-page":"979","DOI":"10.1016\/j.cell.2012.04.024","volume":"149","author":"S Nik-Zainal","year":"2012","unstructured":"Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979\u2013993 (2012).","journal-title":"Cell"},{"key":"BFnm4292_CR30","doi-asserted-by":"publisher","first-page":"994","DOI":"10.1016\/j.cell.2012.04.023","volume":"149","author":"S Nik-Zainal","year":"2012","unstructured":"Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994\u20131007 (2012).","journal-title":"Cell"},{"key":"BFnm4292_CR31","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nature12477","volume":"500","author":"LB Alexandrov","year":"2013","unstructured":"Alexandrov, L.B. et al. Signatures of mutational processes in human cancer. Nature 500, 415\u2013421 (2013).","journal-title":"Nature"},{"key":"BFnm4292_CR32","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1038\/nature14169","volume":"518","author":"N Waddell","year":"2015","unstructured":"Waddell, N. et al. Whole genomes redefine the mutational landscape of pancreatic cancer. Nature 518, 495\u2013501 (2015).","journal-title":"Nature"},{"key":"BFnm4292_CR33","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1038\/nature16965","volume":"531","author":"P Bailey","year":"2016","unstructured":"Bailey, P. et al. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature 531, 47\u201352 (2016).","journal-title":"Nature"},{"key":"BFnm4292_CR34","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1038\/nature14410","volume":"521","author":"AM Patch","year":"2015","unstructured":"Patch, A.M. et al. Whole-genome characterization of chemoresistant ovarian cancer. Nature 521, 489\u2013494 (2015).","journal-title":"Nature"},{"key":"BFnm4292_CR35","doi-asserted-by":"publisher","first-page":"8683","DOI":"10.1038\/ncomms9683","volume":"6","author":"LB Alexandrov","year":"2015","unstructured":"Alexandrov, L.B., Nik-Zainal, S., Siu, H.C., Leung, S.Y. & Stratton, M.R. A mutational signature in gastric cancer suggests therapeutic strategies. Nat. Commun. 6, 8683 (2015).","journal-title":"Nat. Commun."},{"key":"BFnm4292_CR36","doi-asserted-by":"publisher","first-page":"R95","DOI":"10.1186\/bcr3020","volume":"13","author":"OA Stefansson","year":"2011","unstructured":"Stefansson, O.A. et al. Genomic and phenotypic analysis of BRCA2 mutated breast cancers reveals co-occurring changes linked to progression. Breast Cancer Res. 13, R95 (2011).","journal-title":"Breast Cancer Res."},{"key":"BFnm4292_CR37","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1038\/nm.3886","volume":"21","author":"LR Yates","year":"2015","unstructured":"Yates, L.R. et al. Subclonal diversification of primary breast cancer revealed by multiregion sequencing. Nat. Med. 21, 751\u2013759 (2015).","journal-title":"Nat. Med."},{"key":"BFnm4292_CR38","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1007\/s10549-010-0983-z","volume":"123","author":"AA Rodriguez","year":"2010","unstructured":"Rodriguez, A.A. et al. DNA repair signature is associated with anthracycline response in triple negative breast cancer patients. Breast Cancer Res. Treat. 123, 189\u2013196 (2010).","journal-title":"Breast Cancer Res. Treat."},{"key":"BFnm4292_CR39","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1136\/jmg.39.8.608","volume":"39","author":"PO Chappuis","year":"2002","unstructured":"Chappuis, P.O. et al. A significant response to neoadjuvant chemotherapy in BRCA1\/2 related breast cancer. J. Med. Genet. 39, 608\u2013610 (2002).","journal-title":"J. Med. Genet."},{"key":"BFnm4292_CR40","doi-asserted-by":"publisher","first-page":"4880","DOI":"10.1158\/0008-5472.CAN-09-4563","volume":"70","author":"MS Lee","year":"2010","unstructured":"Lee, M.S. et al. Comprehensive analysis of missense variations in the BRCT domain of BRCA1 by structural and functional assays. Cancer Res. 70, 4880\u20134890 (2010).","journal-title":"Cancer Res."},{"key":"BFnm4292_CR41","doi-asserted-by":"publisher","first-page":"1111","DOI":"10.1038\/nature06548","volume":"451","author":"SL Edwards","year":"2008","unstructured":"Edwards, S.L. et al. Resistance to therapy caused by intragenic deletion in BRCA2. Nature 451, 1111\u20131115 (2008).","journal-title":"Nature"},{"key":"BFnm4292_CR42","doi-asserted-by":"publisher","first-page":"1116","DOI":"10.1038\/nature06633","volume":"451","author":"W Sakai","year":"2008","unstructured":"Sakai, W. et al. Secondary mutations as a mechanism of cisplatin resistance in BRCA2-mutated cancers. Nature 451, 1116\u20131120 (2008).","journal-title":"Nature"},{"key":"BFnm4292_CR43","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows\u2013Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"BFnm4292_CR44","doi-asserted-by":"publisher","first-page":"2865","DOI":"10.1093\/bioinformatics\/btp394","volume":"25","author":"K Ye","year":"2009","unstructured":"Ye, K., Schulz, M.H., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865\u20132871 (2009).","journal-title":"Bioinformatics"},{"key":"BFnm4292_CR45","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1101\/gr.074492.107","volume":"18","author":"DR Zerbino","year":"2008","unstructured":"Zerbino, D.R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821\u2013829 (2008).","journal-title":"Genome Res."},{"key":"BFnm4292_CR46","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1016\/j.celrep.2012.12.008","volume":"3","author":"LB Alexandrov","year":"2013","unstructured":"Alexandrov, L.B., Nik-Zainal, S., Wedge, D.C., Campbell, P.J. & Stratton, M.R. Deciphering signatures of mutational processes operative in human cancer. Cell Reports 3, 246\u2013259 (2013).","journal-title":"Cell Reports"},{"key":"BFnm4292_CR47","doi-asserted-by":"publisher","first-page":"1402","DOI":"10.1038\/ng.3441","volume":"47","author":"LB Alexandrov","year":"2015","unstructured":"Alexandrov, L.B. et al. Clock-like mutational processes in human somatic cells. Nat. Genet. 47, 1402\u20131407 (2015).","journal-title":"Nat. Genet."},{"key":"BFnm4292_CR48","doi-asserted-by":"publisher","first-page":"16910","DOI":"10.1073\/pnas.1009843107","volume":"107","author":"P Van Loo","year":"2010","unstructured":"Van Loo, P. et al. Allele-specific copy number analysis of tumors. Proc. Natl. Acad. Sci. USA 107, 16910\u201316915 (2010).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFnm4292_CR49","doi-asserted-by":"publisher","first-page":"1776","DOI":"10.1038\/bjc.2012.451","volume":"107","author":"V Abkevich","year":"2012","unstructured":"Abkevich, V. et al. Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer. Br. J. Cancer 107, 1776\u20131782 (2012).","journal-title":"Br. J. Cancer"},{"key":"BFnm4292_CR50","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1002\/path.4325","volume":"232","author":"R Natrajan","year":"2014","unstructured":"Natrajan, R. et al. Characterization of the genomic features and expressed fusion genes in micropapillary carcinomas of the breast. J. Pathol. 232, 553\u2013565 (2014).","journal-title":"J. Pathol."},{"key":"BFnm4292_CR51","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","volume":"58","author":"R Tibshirani","year":"1996","unstructured":"Tibshirani, R. Regression shrinkage and selection via the lasso. J. R. Stat. Soc. Series B Stat. Methodol. 58, 267\u2013288 (1996).","journal-title":"J. R. Stat. Soc. Series B Stat. Methodol."}],"container-title":["Nature Medicine"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/nm.4292.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nm.4292","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/nm.4292.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,22]],"date-time":"2024-06-22T19:20:08Z","timestamp":1719084008000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/nm.4292"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3,13]]},"references-count":51,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2017,4]]}},"alternative-id":["BFnm4292"],"URL":"https:\/\/doi.org\/10.1038\/nm.4292","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.727392893.793552753","asserted-by":"object"},{"id-type":"doi","id":"10.3410\/f.727392893.793550423","asserted-by":"object"},{"id-type":"doi","id":"10.3410\/f.727392893.793532126","asserted-by":"object"}]},"ISSN":["1078-8956","1546-170X"],"issn-type":[{"value":"1078-8956","type":"print"},{"value":"1546-170X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,3,13]]},"assertion":[{"value":"8 November 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 January 2017","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 March 2017","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"H. Davies, D. Glodzik and S. Nik-Zainal are inventors on a patent application encompassing the code and intellectual principle on this algorithm. The patent has been filed with UK IPO. A.T. has been in receipt of payments from the Institute of Cancer Research Rewards to inventors scheme associated with the invention of PARP inhibitors as therapy for <i>BRCA1<\/i>- and <i>BRCA2<\/i>\u2013mutation-associated cancers.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}