1. Easton, D. F. et al. Gene-panel sequencing and the prediction of breast-cancer risk. N. Engl. J. Med. 372, 2243–2257 (2015).
2. Tung, N. et al. Frequency of germline mutations in 25 cancer susceptibility genes in a sequential series of patients with breast cancer. J. Clin. Oncol. 34, 1460–1468 (2016).
3. Sun, J. et al. Germline mutations in cancer susceptibility genes in a large series of unselected breast cancer patients. Clin. Cancer Res. 23, 6113–6119 (2017).
4. Momozawa, Y. et al. Germline pathogenic variants of 11 breast cancer genes in 7,051 Japanese patients and 11,241 controls. Nat. Commun. 9, 4083 (2018).
5. Sugano, K. et al. Cross-sectional analysis of germline BRCA1 and BRCA2 mutations in Japanese patients suspected to have hereditary breast/ovarian cancer. Cancer Sci. 99, 1967–1976 (2008).
6. Nakamura, S. et al. Prevalence and differentiation of hereditary breast and ovarian cancers in Japan. Breast Cancer 22, 462–468 (2015).
7. Polak, P. et al. A mutational signature reveals alterations underlying deficient homologous recombination repair in breast cancer. Nat. Genet. 49, 1476–1486 (2017).
8. Nik-Zainal, S. et al. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 534, 47–54 (2016).
9. Nielsen, F. C., van Overeem Hansen, T. & Sørensen, C. S. Hereditary breast and ovarian cancer: new genes in confined pathways. Nat. Rev. Cancer 16, 599–612 (2016).
10. Maxwell, K. N. et al. BRCA locus-specific loss of heterozygosity in germline BRCA1 and BRCA2 carriers. Nat. Commun. 8, 319 (2017).
11. Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61–70 (2012).
12. Stephens, P. J. et al. The landscape of cancer genes and mutational processes in breast cancer. Nature 486, 400–404 (2012).
13. Banerji, S. et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature 486, 405–409 (2012).
14. Shah, S. P. et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 486, 395–399 (2012).
15. Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994–1007 (2012).
16. Sanchez-Garcia, F. et al. Integration of genomic data enables selective discovery of breast cancer drivers. Cell 159, 1461–1475 (2014).
17. Antoniou, A. C. et al. Breast-cancer risk in families with mutations in PALB2. N. Engl. J. Med. 371, 497–506 (2014).
18. Couch, F. J. et al. Inherited mutations in 17 breast cancer susceptibility genes among a large triple-negative breast cancer cohort unselected for family history of breast cancer. J. Clin. Oncol. 33, 304–311 (2015).
19. Sekine, M. et al. Mutational analysis of BRCA1 and BRCA2 and clinicopathologic analysis of ovarian cancer in 82 ovarian cancer families: two common founder mutations of BRCA1 in Japanese population. Clin. Cancer Res. 7, 3144–3150 (2001).
20. Kim, Y. C. et al. Prevalence and spectrum of BRCA germline variants in mainland Chinese familial breast and ovarian cancer patients. Oncotarget 7, 9600–9612 (2016).
21. Daly, M., Pilarski, R. & Berry, M. NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines®Genetic/Familial High-Risk Assessment: Breast and Ovarian Version 1, 2018).
22. Shiraishi, Y., Tremmel, G., Miyano, S. & Stephens, M. A simple model-based approach to inferring and visualizing cancer mutation signatures. PLoS Genet. 11, e1005657 (2015).
23. Sorlie, T. et al. Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc. Natl Acad. Sci. USA 100, 8418–8423 (2003).
24. Foulkes, W. D. et al. Germline BRCA1 mutations and a basal epithelial phenotype in breast cancer. J. Natl Cancer Inst. 95, 1482–1485 (2003).
25. Martins, F. C. et al. Evolutionary pathways in BRCA1-associated breast tumors. Cancer Discov. 2, 503–511 (2012).
26. Skoulidis, F. et al. Germline Brca2 heterozygosity promotes Kras(G12D)-driven carcinogenesis in a murine model of familial pancreatic cancer. Cancer Cell 18, 499–509 (2010).
27. Konishi, H. et al. Mutation of a single allele of the cancer susceptibility gene BRCA1 leads to genomic instability in human breast epithelial cells. Proc. Natl Acad. Sci. USA 108, 17773–17778 (2011).
28. Tutt, A. et al. Carboplatin in BRCA1/2-mutated and triple-negative breast cancer BRCAness subgroups: the TNT Trial. Nat. Med. 24, 628–637 (2018).
29. Robson, M. et al. Olaparib for metastatic breast cancer in patients with a germline BRCA mutation. N. Engl. J. Med. 377, 523–533 (2017).
30. Farmer, H. et al. Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy. Nature 434, 917–921 (2005).
31. Drew, Y. et al. Therapeutic potential of poly(ADP-ribose) polymerase inhibitor AG014699 in human cancers with mutated or methylated BRCA1 or BRCA2. J. Natl Cancer Inst. 103, 334–346 (2011).
32. Jonsson, P. et al. Tumour lineage shapes BRCA-mediated phenotypes. Nature 571, 576–579 (2019).
33. Bernard, E. et al. Implications of TP53 allelic state for genome stability, clinical presentation and outcomes in myelodysplastic syndromes. Nat. Med. 26, 1549–1556 (2020).
34. Calvo, S. E. et al. High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nat. Genet. 42, 851–858 (2010).
35. Shiraishi, Y. et al. An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. Nucleic Acids Res. 41, e89 (2013).
36. Yoshida, K. et al. The landscape of somatic mutations in Down syndrome- related myeloid disorders. Nat. Genet. 45, 1293–1299 (2013).
37. Pritchard, C. C. et al. Inherited DNA-repair gene mutations in men with metastatic prostate cancer. N. Engl. J. Med. 375, 443–453 (2016).
38. Zhang, J. et al. Germline mutations in predisposition genes in pediatric cancer. N. Engl. J. Med. 373, 2336–2346 (2015).
39. Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213–219 (2013).
40. Yokoyama, A. et al. Age-related remodelling of oesophageal epithelia by mutated cancer drivers. Nature 565, 312–317 (2019).
41. Boeva, V. et al. Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics 28, 423–425 (2012).
42. Nannya, Y. et al. A robust algorithm for copy number detection using high- density oligonucleotide single nucleotide polymorphism genotyping arrays. Cancer Res. 65, 6071–6079 (2005).
43. Yamamoto, G. et al. Highly sensitive method for genomewide detection of allelic composition in nonpaired, primary tumor specimens by use of affymetrix single-nucleotide-polymorphism genotyping microarrays. Am. J. Hum. Genet. 81, 114–126 (2007).
44. Kataoka, K. et al. Aberrant PD-L1 expression through 3’-UTR disruption in multiple cancers. Nature 534, 402–406 (2016).