Panel sequencing of 264 candidate susceptibility genes and segregation analysis in a cohort of non-BRCA1, non-BRCA2 breast cancer families

go back to reference Lalloo F, Evans DG (2012) Familial breast cancer. Clin Genet 82(2):105–114. doi:10.1111/j.1399-0004.2012.01859.x CrossRefPubMed Lalloo F, Evans DG (2012) Familial breast cancer. Clin Genet 82(2):105–114. doi:10.​1111/​j.​1399-0004.​2012.​01859.​x CrossRefPubMed

go back to reference Ford D, Easton DF, Stratton M, Narod S, Goldgar D, Devilee P, Bishop DT, Weber B, Lenoir G, Chang-Claude J, Sobol H, Teare MD, Struewing J, Arason A, Scherneck S, Peto J, Rebbeck TR, Tonin P, Neuhausen S, Barkardottir R, Eyfjord J, Lynch H, Ponder BA, Gayther SA, Zelada-Hedman M et al (1998) Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. Am J Hum Genet 62(3):676–689CrossRefPubMedPubMedCentral Ford D, Easton DF, Stratton M, Narod S, Goldgar D, Devilee P, Bishop DT, Weber B, Lenoir G, Chang-Claude J, Sobol H, Teare MD, Struewing J, Arason A, Scherneck S, Peto J, Rebbeck TR, Tonin P, Neuhausen S, Barkardottir R, Eyfjord J, Lynch H, Ponder BA, Gayther SA, Zelada-Hedman M et al (1998) Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. Am J Hum Genet 62(3):676–689CrossRefPubMedPubMedCentral

go back to reference Easton DF, Pharoah PD, Antoniou AC, Tischkowitz M, Tavtigian SV, Nathanson KL, Devilee P, Meindl A, Couch FJ, Southey M, Goldgar DE, Evans DG, Chenevix-Trench G, Rahman N, Robson M, Domchek SM, Foulkes WD (2015) Gene-panel sequencing and the prediction of breast-cancer risk. N Engl J Med 372(23):2243–2257. doi:10.1056/NEJMsr1501341 CrossRefPubMedPubMedCentral Easton DF, Pharoah PD, Antoniou AC, Tischkowitz M, Tavtigian SV, Nathanson KL, Devilee P, Meindl A, Couch FJ, Southey M, Goldgar DE, Evans DG, Chenevix-Trench G, Rahman N, Robson M, Domchek SM, Foulkes WD (2015) Gene-panel sequencing and the prediction of breast-cancer risk. N Engl J Med 372(23):2243–2257. doi:10.​1056/​NEJMsr1501341 CrossRefPubMedPubMedCentral

go back to reference Wen H, Kim YC, Snyder C, Xiao F, Fleissner EA, Becirovic D, Luo J, Downs B, Sherman S, Cowan KH, Lynch HT, Wang SM (2014) Family-specific, novel, deleterious germline variants provide a rich resource to identify genetic predispositions for BRCAx familial breast cancer. BMC cancer 14:470. doi:10.1186/1471-2407-14-470 CrossRefPubMedPubMedCentral Wen H, Kim YC, Snyder C, Xiao F, Fleissner EA, Becirovic D, Luo J, Downs B, Sherman S, Cowan KH, Lynch HT, Wang SM (2014) Family-specific, novel, deleterious germline variants provide a rich resource to identify genetic predispositions for BRCAx familial breast cancer. BMC cancer 14:470. doi:10.​1186/​1471-2407-14-470 CrossRefPubMedPubMedCentral

go back to reference Sun J, Wang Y, Xia Y, Xu Y, Ouyang T, Li J, Wang T, Fan Z, Fan T, Lin B, Lou H, Xie Y (2015) Mutations in RECQL gene are associated with predisposition to breast cancer. PLoS Genet 11(5):e1005228. doi:10.1371/journal.pgen.1005228 CrossRefPubMedPubMedCentral Sun J, Wang Y, Xia Y, Xu Y, Ouyang T, Li J, Wang T, Fan Z, Fan T, Lin B, Lou H, Xie Y (2015) Mutations in RECQL gene are associated with predisposition to breast cancer. PLoS Genet 11(5):e1005228. doi:10.​1371/​journal.​pgen.​1005228 CrossRefPubMedPubMedCentral

go back to reference Cybulski C, Carrot-Zhang J, Kluzniak W, Rivera B, Kashyap A, Wokolorczyk D, Giroux S, Nadaf J, Hamel N, Zhang S, Huzarski T, Gronwald J, Byrski T, Szwiec M, Jakubowska A, Rudnicka H, Lener M, Masojc B, Tonin PN, Rousseau F, Gorski B, Debniak T, Majewski J, Lubinski J, Foulkes WD, Narod SA, Akbari MR (2015) Germline RECQL mutations are associated with breast cancer susceptibility. Nat Genet 47(6):643–646. doi:10.1038/ng.3284 CrossRefPubMed Cybulski C, Carrot-Zhang J, Kluzniak W, Rivera B, Kashyap A, Wokolorczyk D, Giroux S, Nadaf J, Hamel N, Zhang S, Huzarski T, Gronwald J, Byrski T, Szwiec M, Jakubowska A, Rudnicka H, Lener M, Masojc B, Tonin PN, Rousseau F, Gorski B, Debniak T, Majewski J, Lubinski J, Foulkes WD, Narod SA, Akbari MR (2015) Germline RECQL mutations are associated with breast cancer susceptibility. Nat Genet 47(6):643–646. doi:10.​1038/​ng.​3284 CrossRefPubMed

go back to reference Carter JM, O’Hara C, Dundas G, Gilchrist D, Collins MS, Eaton K, Judkins AR, Biegel JA, Folpe AL (2012) Epithelioid malignant peripheral nerve sheath tumor arising in a schwannoma, in a patient with “neuroblastoma-like” schwannomatosis and a novel germline SMARCB1 mutation. Am J Surg Pathol 36(1):154–160. doi:10.1097/PAS.0b013e3182380802 CrossRefPubMedPubMedCentral Carter JM, O’Hara C, Dundas G, Gilchrist D, Collins MS, Eaton K, Judkins AR, Biegel JA, Folpe AL (2012) Epithelioid malignant peripheral nerve sheath tumor arising in a schwannoma, in a patient with “neuroblastoma-like” schwannomatosis and a novel germline SMARCB1 mutation. Am J Surg Pathol 36(1):154–160. doi:10.​1097/​PAS.​0b013e3182380802​ CrossRefPubMedPubMedCentral

go back to reference Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Borresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S (2017) A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers. Nat Genet 49(3):341–348. doi:10.1038/ng.3771 CrossRefPubMed Glodzik D, Morganella S, Davies H, Simpson PT, Li Y, Zou X, Diez-Perez J, Staaf J, Alexandrov LB, Smid M, Brinkman AB, Rye IH, Russnes H, Raine K, Purdie CA, Lakhani SR, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Borresen-Dale AL, Richardson AL, Kong G, Viari A, Easton D, Evan G, Campbell PJ, Stratton MR, Nik-Zainal S (2017) A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers. Nat Genet 49(3):341–348. doi:10.​1038/​ng.​3771 CrossRefPubMed

go back to reference Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L (2014) Integrated analysis of germline and somatic variants in ovarian cancer. Nat Commun 5:3156. doi:10.1038/ncomms4156 CrossRefPubMedPubMedCentral Kanchi KL, Johnson KJ, Lu C, McLellan MD, Leiserson MD, Wendl MC, Zhang Q, Koboldt DC, Xie M, Kandoth C, McMichael JF, Wyczalkowski MA, Larson DE, Schmidt HK, Miller CA, Fulton RS, Spellman PT, Mardis ER, Druley TE, Graubert TA, Goodfellow PJ, Raphael BJ, Wilson RK, Ding L (2014) Integrated analysis of germline and somatic variants in ovarian cancer. Nat Commun 5:3156. doi:10.​1038/​ncomms4156 CrossRefPubMedPubMedCentral

go back to reference Liao L, Testa JR, Yang H (2015) The roles of chromatin-remodelers and epigenetic modifiers in kidney cancer. Cancer Genet 208(5):206–214. doi:10.1016/j.cancergen.2015.02.008 CrossRefPubMedPubMedCentral Liao L, Testa JR, Yang H (2015) The roles of chromatin-remodelers and epigenetic modifiers in kidney cancer. Cancer Genet 208(5):206–214. doi:10.​1016/​j.​cancergen.​2015.​02.​008 CrossRefPubMedPubMedCentral

go back to reference Jhanwar SC (2015) Genetic and epigenetic pathways in myelodysplastic syndromes: a brief overview. Adv Biol Regul 58:28–37. doi:10.1016/j.jbior.2014.11.002 CrossRefPubMed Jhanwar SC (2015) Genetic and epigenetic pathways in myelodysplastic syndromes: a brief overview. Adv Biol Regul 58:28–37. doi:10.​1016/​j.​jbior.​2014.​11.​002 CrossRefPubMed

go back to reference Cazzola M, Della Porta MG, Malcovati L (2013) The genetic basis of myelodysplasia and its clinical relevance. Blood 122(25):4021–4034. doi:10.1182/blood-2013-09-381665 CrossRefPubMedPubMedCentral Cazzola M, Della Porta MG, Malcovati L (2013) The genetic basis of myelodysplasia and its clinical relevance. Blood 122(25):4021–4034. doi:10.​1182/​blood-2013-09-381665 CrossRefPubMedPubMedCentral

go back to reference Lee RS, Roberts CW (2013) Rhabdoid tumors: an initial clue to the role of chromatin remodeling in cancer. Brain Pathol 23(2):200–205. doi:10.1111/bpa.12021 CrossRefPubMed Lee RS, Roberts CW (2013) Rhabdoid tumors: an initial clue to the role of chromatin remodeling in cancer. Brain Pathol 23(2):200–205. doi:10.​1111/​bpa.​12021 CrossRefPubMed

go back to reference Ratnakumar K, Bernstein E (2013) ATRX: the case of a peculiar chromatin remodeler. Epigenetics 8(1):3–9. doi:10.4161/epi.23271 CrossRefPubMedPubMedCentral Ratnakumar K, Bernstein E (2013) ATRX: the case of a peculiar chromatin remodeler. Epigenetics 8(1):3–9. doi:10.​4161/​epi.​23271 CrossRefPubMedPubMedCentral

go back to reference Koschmann C, Nunez FJ, Mendez F, Brosnan-Cashman JA, Meeker AK, Lowenstein PR, Castro MG (2017) Mutated chromatin regulatory factors as tumor drivers in cancer. Cancer Res 77(2):227–233. doi:10.1158/0008-5472.CAN-16-2301 CrossRefPubMedPubMedCentral Koschmann C, Nunez FJ, Mendez F, Brosnan-Cashman JA, Meeker AK, Lowenstein PR, Castro MG (2017) Mutated chromatin regulatory factors as tumor drivers in cancer. Cancer Res 77(2):227–233. doi:10.​1158/​0008-5472.​CAN-16-2301 CrossRefPubMedPubMedCentral

go back to reference Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjaerde OC, Langerod A, Ringner M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GK, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O’Meara S, Pauporte I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodriguez-Gonzalez FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van’t Veer L, Tutt A, Knappskog S, Tan BK, Jonkers J, Borg A, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Borresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR (2016) Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 534(7605):47–54. doi:10.1038/nature17676 CrossRefPubMedPubMedCentral Nik-Zainal S, Davies H, Staaf J, Ramakrishna M, Glodzik D, Zou X, Martincorena I, Alexandrov LB, Martin S, Wedge DC, Van Loo P, Ju YS, Smid M, Brinkman AB, Morganella S, Aure MR, Lingjaerde OC, Langerod A, Ringner M, Ahn SM, Boyault S, Brock JE, Broeks A, Butler A, Desmedt C, Dirix L, Dronov S, Fatima A, Foekens JA, Gerstung M, Hooijer GK, Jang SJ, Jones DR, Kim HY, King TA, Krishnamurthy S, Lee HJ, Lee JY, Li Y, McLaren S, Menzies A, Mustonen V, O’Meara S, Pauporte I, Pivot X, Purdie CA, Raine K, Ramakrishnan K, Rodriguez-Gonzalez FG, Romieu G, Sieuwerts AM, Simpson PT, Shepherd R, Stebbings L, Stefansson OA, Teague J, Tommasi S, Treilleux I, Van den Eynden GG, Vermeulen P, Vincent-Salomon A, Yates L, Caldas C, van’t Veer L, Tutt A, Knappskog S, Tan BK, Jonkers J, Borg A, Ueno NT, Sotiriou C, Viari A, Futreal PA, Campbell PJ, Span PN, Van Laere S, Lakhani SR, Eyfjord JE, Thompson AM, Birney E, Stunnenberg HG, van de Vijver MJ, Martens JW, Borresen-Dale AL, Richardson AL, Kong G, Thomas G, Stratton MR (2016) Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 534(7605):47–54. doi:10.​1038/​nature17676 CrossRefPubMedPubMedCentral

go back to reference Blewitt ME, Gendrel AV, Pang Z, Sparrow DB, Whitelaw N, Craig JM, Apedaile A, Hilton DJ, Dunwoodie SL, Brockdorff N, Kay GF, Whitelaw E (2008) SmcHD1, containing a structural-maintenance-of-chromosomes hinge domain, has a critical role in X inactivation. Nat Genet 40(5):663–669. doi:10.1038/ng.142 CrossRefPubMed Blewitt ME, Gendrel AV, Pang Z, Sparrow DB, Whitelaw N, Craig JM, Apedaile A, Hilton DJ, Dunwoodie SL, Brockdorff N, Kay GF, Whitelaw E (2008) SmcHD1, containing a structural-maintenance-of-chromosomes hinge domain, has a critical role in X inactivation. Nat Genet 40(5):663–669. doi:10.​1038/​ng.​142 CrossRefPubMed

go back to reference Ashe A, Morgan DK, Whitelaw NC, Bruxner TJ, Vickaryous NK, Cox LL, Butterfield NC, Wicking C, Blewitt ME, Wilkins SJ, Anderson GJ, Cox TC, Whitelaw E (2008) A genome-wide screen for modifiers of transgene variegation identifies genes with critical roles in development. Genome Biol 9(12):R182. doi:10.1186/gb-2008-9-12-r182 CrossRefPubMedPubMedCentral Ashe A, Morgan DK, Whitelaw NC, Bruxner TJ, Vickaryous NK, Cox LL, Butterfield NC, Wicking C, Blewitt ME, Wilkins SJ, Anderson GJ, Cox TC, Whitelaw E (2008) A genome-wide screen for modifiers of transgene variegation identifies genes with critical roles in development. Genome Biol 9(12):R182. doi:10.​1186/​gb-2008-9-12-r182 CrossRefPubMedPubMedCentral

go back to reference Whitelaw NC, Chong S, Morgan DK, Nestor C, Bruxner TJ, Ashe A, Lambley E, Meehan R, Whitelaw E (2010) Reduced levels of two modifiers of epigenetic gene silencing, Dnmt3a and Trim28, cause increased phenotypic noise. Genome Biol 11(11):R111. doi:10.1186/gb-2010-11-11-r111 CrossRefPubMedPubMedCentral Whitelaw NC, Chong S, Morgan DK, Nestor C, Bruxner TJ, Ashe A, Lambley E, Meehan R, Whitelaw E (2010) Reduced levels of two modifiers of epigenetic gene silencing, Dnmt3a and Trim28, cause increased phenotypic noise. Genome Biol 11(11):R111. doi:10.​1186/​gb-2010-11-11-r111 CrossRefPubMedPubMedCentral

go back to reference Daxinger L, Oey H, Apedaile A, Sutton J, Ashe A, Whitelaw E (2012) A forward genetic screen identifies eukaryotic translation initiation factor 3, subunit H (eIF3h), as an enhancer of variegation in the mouse. G3 (Bethesda) 2(11):1393–1396. doi:10.1534/g3.112.004036 CrossRef Daxinger L, Oey H, Apedaile A, Sutton J, Ashe A, Whitelaw E (2012) A forward genetic screen identifies eukaryotic translation initiation factor 3, subunit H (eIF3h), as an enhancer of variegation in the mouse. G3 (Bethesda) 2(11):1393–1396. doi:10.​1534/​g3.​112.​004036 CrossRef

go back to reference Flanagan JM, Cocciardi S, Waddell N, Johnstone CN, Marsh A, Henderson S, Simpson P, da Silva L, kConFab I, Khanna K, Lakhani S, Boshoff C, Chenevix-Trench G (2010) DNA methylome of familial breast cancer identifies distinct profiles defined by mutation status. Am J Hum Genet 86(3):420–433. doi:10.1016/j.ajhg.2010.02.008 CrossRefPubMedPubMedCentral Flanagan JM, Cocciardi S, Waddell N, Johnstone CN, Marsh A, Henderson S, Simpson P, da Silva L, kConFab I, Khanna K, Lakhani S, Boshoff C, Chenevix-Trench G (2010) DNA methylome of familial breast cancer identifies distinct profiles defined by mutation status. Am J Hum Genet 86(3):420–433. doi:10.​1016/​j.​ajhg.​2010.​02.​008 CrossRefPubMedPubMedCentral

go back to reference Shukla V, Coumoul X, Lahusen T, Wang RH, Xu X, Vassilopoulos A, Xiao C, Lee MH, Man YG, Ouchi M, Ouchi T, Deng CX (2010) BRCA1 affects global DNA methylation through regulation of DNMT1. Cell Res 20(11):1201–1215. doi:10.1038/cr.2010.128 CrossRefPubMed Shukla V, Coumoul X, Lahusen T, Wang RH, Xu X, Vassilopoulos A, Xiao C, Lee MH, Man YG, Ouchi M, Ouchi T, Deng CX (2010) BRCA1 affects global DNA methylation through regulation of DNMT1. Cell Res 20(11):1201–1215. doi:10.​1038/​cr.​2010.​128 CrossRefPubMed

go back to reference Hitchins MP, Wong JJ, Suthers G, Suter CM, Martin DI, Hawkins NJ, Ward RL (2007) Inheritance of a cancer-associated MLH1 germ-line epimutation. N Engl J Med 356(7):697–705. doi:10.1056/NEJMoa064522 CrossRefPubMed Hitchins MP, Wong JJ, Suthers G, Suter CM, Martin DI, Hawkins NJ, Ward RL (2007) Inheritance of a cancer-associated MLH1 germ-line epimutation. N Engl J Med 356(7):697–705. doi:10.​1056/​NEJMoa064522 CrossRefPubMed

go back to reference Mann GJ, Thorne H, Balleine RL, Butow PN, Clarke CL, Edkins E, Evans GM, Fereday S, Haan E, Gattas M, Giles GG, Goldblatt J, Hopper JL, Kirk J, Leary JA, Lindeman G, Niedermayr E, Phillips KA, Picken S, Pupo GM, Saunders C, Scott CL, Spurdle AB, Suthers G, Tucker K, Chenevix-Trench G, Kathleen Cuningham Consortium for Research in Familial Breast C (2006) Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource. Breast Cancer Res BCR 8(1):R12. doi:10.1186/bcr1377 CrossRefPubMed Mann GJ, Thorne H, Balleine RL, Butow PN, Clarke CL, Edkins E, Evans GM, Fereday S, Haan E, Gattas M, Giles GG, Goldblatt J, Hopper JL, Kirk J, Leary JA, Lindeman G, Niedermayr E, Phillips KA, Picken S, Pupo GM, Saunders C, Scott CL, Spurdle AB, Suthers G, Tucker K, Chenevix-Trench G, Kathleen Cuningham Consortium for Research in Familial Breast C (2006) Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource. Breast Cancer Res BCR 8(1):R12. doi:10.​1186/​bcr1377 CrossRefPubMed

go back to reference Antoniou AC, Cunningham AP, Peto J, Evans DG, Lalloo F, Narod SA, Risch HA, Eyfjord JE, Hopper JL, Southey MC, Olsson H, Johannsson O, Borg A, Pasini B, Radice P, Manoukian S, Eccles DM, Tang N, Olah E, Anton-Culver H, Warner E, Lubinski J, Gronwald J, Gorski B, Tryggvadottir L, Syrjakoski K, Kallioniemi OP, Eerola H, Nevanlinna H, Pharoah PD, Easton DF (2008) The BOADICEA model of genetic susceptibility to breast and ovarian cancers: updates and extensions. Br J Cancer 98(8):1457–1466. doi:10.1038/sj.bjc.6604305 CrossRefPubMedPubMedCentral Antoniou AC, Cunningham AP, Peto J, Evans DG, Lalloo F, Narod SA, Risch HA, Eyfjord JE, Hopper JL, Southey MC, Olsson H, Johannsson O, Borg A, Pasini B, Radice P, Manoukian S, Eccles DM, Tang N, Olah E, Anton-Culver H, Warner E, Lubinski J, Gronwald J, Gorski B, Tryggvadottir L, Syrjakoski K, Kallioniemi OP, Eerola H, Nevanlinna H, Pharoah PD, Easton DF (2008) The BOADICEA model of genetic susceptibility to breast and ovarian cancers: updates and extensions. Br J Cancer 98(8):1457–1466. doi:10.​1038/​sj.​bjc.​6604305 CrossRefPubMedPubMedCentral

go back to reference John EM, Hopper JL, Beck JC, Knight JA, Neuhausen SL, Senie RT, Ziogas A, Andrulis IL, Anton-Culver H, Boyd N, Buys SS, Daly MB, O’Malley FP, Santella RM, Southey MC, Venne VL, Venter DJ, West DW, Whittemore AS, Seminara D, Breast Cancer Family R (2004) The Breast Cancer Family Registry: an infrastructure for cooperative multinational, interdisciplinary and translational studies of the genetic epidemiology of breast cancer. Breast Cancer Research: Bcr 6(4):R375–R389. doi:10.1186/bcr801 CrossRefPubMedPubMedCentral John EM, Hopper JL, Beck JC, Knight JA, Neuhausen SL, Senie RT, Ziogas A, Andrulis IL, Anton-Culver H, Boyd N, Buys SS, Daly MB, O’Malley FP, Santella RM, Southey MC, Venne VL, Venter DJ, West DW, Whittemore AS, Seminara D, Breast Cancer Family R (2004) The Breast Cancer Family Registry: an infrastructure for cooperative multinational, interdisciplinary and translational studies of the genetic epidemiology of breast cancer. Breast Cancer Research: Bcr 6(4):R375–R389. doi:10.​1186/​bcr801 CrossRefPubMedPubMedCentral

go back to reference Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754–1760. doi:10.1093/bioinformatics/btp324 CrossRefPubMedPubMedCentral Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25(14):1754–1760. doi:10.​1093/​bioinformatics/​btp324 CrossRefPubMedPubMedCentral

go back to reference McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297–1303. doi:10.1101/gr.107524.110 CrossRefPubMedPubMedCentral McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297–1303. doi:10.​1101/​gr.​107524.​110 CrossRefPubMedPubMedCentral

go back to reference MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C, Genomes Project C (2012) A systematic survey of loss-of-function variants in human protein-coding genes. Science 335(6070):823–828. doi:10.1126/science.1215040 CrossRefPubMedPubMedCentral MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C, Genomes Project C (2012) A systematic survey of loss-of-function variants in human protein-coding genes. Science 335(6070):823–828. doi:10.​1126/​science.​1215040 CrossRefPubMedPubMedCentral

go back to reference Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, Nik-Zainal S, Martin S, Varela I, Bignell GR, Yates LR, Papaemmanuil E, Beare D, Butler A, Cheverton A, Gamble J, Hinton J, Jia M, Jayakumar A, Jones D, Latimer C, Lau KW, McLaren S, McBride DJ, Menzies A, Mudie L, Raine K, Rad R, Chapman MS, Teague J, Easton D, Langerod A, Oslo Breast Cancer C, Lee MT, Shen CY, Tee BT, Huimin BW, Broeks A, Vargas AC, Turashvili G, Martens J, Fatima A, Miron P, Chin SF, Thomas G, Boyault S, Mariani O, Lakhani SR, van de Vijver M, van ‘t Veer L, Foekens J, Desmedt C, Sotiriou C, Tutt A, Caldas C, Reis-Filho JS, Aparicio SA, Salomon AV, Borresen-Dale AL, Richardson AL, Campbell PJ, Futreal PA, Stratton MR (2012) The landscape of cancer genes and mutational processes in breast cancer. Nature 486(7403):400–404. doi:10.1038/nature11017 PubMedPubMedCentral Stephens PJ, Tarpey PS, Davies H, Van Loo P, Greenman C, Wedge DC, Nik-Zainal S, Martin S, Varela I, Bignell GR, Yates LR, Papaemmanuil E, Beare D, Butler A, Cheverton A, Gamble J, Hinton J, Jia M, Jayakumar A, Jones D, Latimer C, Lau KW, McLaren S, McBride DJ, Menzies A, Mudie L, Raine K, Rad R, Chapman MS, Teague J, Easton D, Langerod A, Oslo Breast Cancer C, Lee MT, Shen CY, Tee BT, Huimin BW, Broeks A, Vargas AC, Turashvili G, Martens J, Fatima A, Miron P, Chin SF, Thomas G, Boyault S, Mariani O, Lakhani SR, van de Vijver M, van ‘t Veer L, Foekens J, Desmedt C, Sotiriou C, Tutt A, Caldas C, Reis-Filho JS, Aparicio SA, Salomon AV, Borresen-Dale AL, Richardson AL, Campbell PJ, Futreal PA, Stratton MR (2012) The landscape of cancer genes and mutational processes in breast cancer. Nature 486(7403):400–404. doi:10.​1038/​nature11017 PubMedPubMedCentral

go back to reference Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S (2012) The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 486(7403):395–399. doi:10.1038/nature10933 PubMed Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, Griffith M, Moradian A, Cheng SW, Morin GB, Watson P, Gelmon K, Chia S, Chin SF, Curtis C, Rueda OM, Pharoah PD, Damaraju S, Mackey J, Hoon K, Harkins T, Tadigotla V, Sigaroudinia M, Gascard P, Tlsty T, Costello JF, Meyer IM, Eaves CJ, Wasserman WW, Jones S, Huntsman D, Hirst M, Caldas C, Marra MA, Aparicio S (2012) The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 486(7403):395–399. doi:10.​1038/​nature10933 PubMed

go back to reference Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38(16):e164. doi:10.1093/nar/gkq603 CrossRefPubMedPubMedCentral Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38(16):e164. doi:10.​1093/​nar/​gkq603 CrossRefPubMedPubMedCentral

go back to reference Kumar P, Henikoff S, Ng PC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4(7):1073–1081. doi:10.1038/nprot.2009.86 CrossRefPubMed Kumar P, Henikoff S, Ng PC (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4(7):1073–1081. doi:10.​1038/​nprot.​2009.​86 CrossRefPubMed

go back to reference Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR (2010) A method and server for predicting damaging missense mutations. Nat Methods 7(4):248–249. doi:10.1038/nmeth0410-248 CrossRefPubMedPubMedCentral Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR (2010) A method and server for predicting damaging missense mutations. Nat Methods 7(4):248–249. doi:10.​1038/​nmeth0410-248 CrossRefPubMedPubMedCentral

go back to reference San Lucas FA, Wang G, Scheet P, Peng B (2012) Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools. Bioinformatics 28(3):421–422. doi:10.1093/bioinformatics/btr667 CrossRefPubMed San Lucas FA, Wang G, Scheet P, Peng B (2012) Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools. Bioinformatics 28(3):421–422. doi:10.​1093/​bioinformatics/​btr667 CrossRefPubMed

go back to reference Schwarz JM, Rodelsperger C, Schuelke M, Seelow D (2010) MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods 7(8):575–576. doi:10.1038/nmeth0810-575 CrossRefPubMed Schwarz JM, Rodelsperger C, Schuelke M, Seelow D (2010) MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods 7(8):575–576. doi:10.​1038/​nmeth0810-575 CrossRefPubMed

go back to reference Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46(3):310–315. doi:10.1038/ng.2892 CrossRefPubMedPubMedCentral Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46(3):310–315. doi:10.​1038/​ng.​2892 CrossRefPubMedPubMedCentral

go back to reference Yeo G, Burge CB (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol J Comput Mol Cell Biol 11(2–3):377–394. doi:10.1089/1066527041410418 CrossRef Yeo G, Burge CB (2004) Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol J Comput Mol Cell Biol 11(2–3):377–394. doi:10.​1089/​1066527041410418​ CrossRef

go back to reference Johnatty SE, Spurdle AB, Beesley J, Chen X, Hopper JL, Duffy DL, Chenevix-Trench G, Kathleen Cuningham Consortium for Research in Familial Breast C (2008) Progesterone receptor polymorphisms and risk of breast cancer: results from two Australian breast cancer studies. Breast Cancer Res Treat 109(1):91–99. doi:10.1007/s10549-007-9627-3 CrossRefPubMed Johnatty SE, Spurdle AB, Beesley J, Chen X, Hopper JL, Duffy DL, Chenevix-Trench G, Kathleen Cuningham Consortium for Research in Familial Breast C (2008) Progesterone receptor polymorphisms and risk of breast cancer: results from two Australian breast cancer studies. Breast Cancer Res Treat 109(1):91–99. doi:10.​1007/​s10549-007-9627-3 CrossRefPubMed

go back to reference Lathrop GM, Lalouel JM, Julier C, Ott J (1985) Multilocus linkage analysis in humans: detection of linkage and estimation of recombination. Am J Hum Genet 37(3):482–498PubMedPubMedCentral Lathrop GM, Lalouel JM, Julier C, Ott J (1985) Multilocus linkage analysis in humans: detection of linkage and estimation of recombination. Am J Hum Genet 37(3):482–498PubMedPubMedCentral

go back to reference Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA, Network TR, Perou CM (2015) Comprehensive molecular portraits of invasive lobular breast cancer. Cell 163(2):506–519. doi:10.1016/j.cell.2015.09.033 CrossRefPubMedPubMedCentral Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA, Network TR, Perou CM (2015) Comprehensive molecular portraits of invasive lobular breast cancer. Cell 163(2):506–519. doi:10.​1016/​j.​cell.​2015.​09.​033 CrossRefPubMedPubMedCentral

go back to reference Pereira B, Chin SF, Rueda OM, Vollan HK, Provenzano E, Bardwell HA, Pugh M, Jones L, Russell R, Sammut SJ, Tsui DW, Liu B, Dawson SJ, Abraham J, Northen H, Peden JF, Mukherjee A, Turashvili G, Green AR, McKinney S, Oloumi A, Shah S, Rosenfeld N, Murphy L, Bentley DR, Ellis IO, Purushotham A, Pinder SE, Borresen-Dale AL, Earl HM, Pharoah PD, Ross MT, Aparicio S, Caldas C (2016) The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Nat Commun 7:11479. doi:10.1038/ncomms11479 CrossRefPubMedPubMedCentral Pereira B, Chin SF, Rueda OM, Vollan HK, Provenzano E, Bardwell HA, Pugh M, Jones L, Russell R, Sammut SJ, Tsui DW, Liu B, Dawson SJ, Abraham J, Northen H, Peden JF, Mukherjee A, Turashvili G, Green AR, McKinney S, Oloumi A, Shah S, Rosenfeld N, Murphy L, Bentley DR, Ellis IO, Purushotham A, Pinder SE, Borresen-Dale AL, Earl HM, Pharoah PD, Ross MT, Aparicio S, Caldas C (2016) The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Nat Commun 7:11479. doi:10.​1038/​ncomms11479 CrossRefPubMedPubMedCentral

go back to reference Cancer Genome Atlas N (2012) Comprehensive molecular portraits of human breast tumours. Nature 490(7418):61–70. doi:10.1038/nature11412 CrossRef Cancer Genome Atlas N (2012) Comprehensive molecular portraits of human breast tumours. Nature 490(7418):61–70. doi:10.​1038/​nature11412 CrossRef

go back to reference Ishihara K, Oshimura M, Nakao M (2006) CTCF-dependent chromatin insulator is linked to epigenetic remodeling. Mol Cell 23(5):733–742. doi:10.1016/j.molcel.2006.08.008 CrossRefPubMed Ishihara K, Oshimura M, Nakao M (2006) CTCF-dependent chromatin insulator is linked to epigenetic remodeling. Mol Cell 23(5):733–742. doi:10.​1016/​j.​molcel.​2006.​08.​008 CrossRefPubMed

go back to reference Kim N, Hong Y, Kwon D, Yoon S (2013) Somatic mutaome profile in human cancer tissues. Genom Inform 11(4):239–244. doi:10.5808/GI.2013.11.4.239 CrossRef Kim N, Hong Y, Kwon D, Yoon S (2013) Somatic mutaome profile in human cancer tissues. Genom Inform 11(4):239–244. doi:10.​5808/​GI.​2013.​11.​4.​239 CrossRef

go back to reference Pongor L, Kormos M, Hatzis C, Pusztai L, Szabo A, Gyorffy B (2015) A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients. Genome Med 7:104. doi:10.1186/s13073-015-0228-1 CrossRefPubMedPubMedCentral Pongor L, Kormos M, Hatzis C, Pusztai L, Szabo A, Gyorffy B (2015) A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients. Genome Med 7:104. doi:10.​1186/​s13073-015-0228-1 CrossRefPubMedPubMedCentral

go back to reference Subtil-Rodriguez A, Vazquez-Chavez E, Ceballos-Chavez M, Rodriguez-Paredes M, Martin-Subero JI, Esteller M, Reyes JC (2014) The chromatin remodeller CHD8 is required for E2F-dependent transcription activation of S-phase genes. Nucleic Acids Res 42(4):2185–2196. doi:10.1093/nar/gkt1161 CrossRefPubMed Subtil-Rodriguez A, Vazquez-Chavez E, Ceballos-Chavez M, Rodriguez-Paredes M, Martin-Subero JI, Esteller M, Reyes JC (2014) The chromatin remodeller CHD8 is required for E2F-dependent transcription activation of S-phase genes. Nucleic Acids Res 42(4):2185–2196. doi:10.​1093/​nar/​gkt1161 CrossRefPubMed

go back to reference Jones S, Wang TL, Shih Ie M, Mao TL, Nakayama K, Roden R, Glas R, Slamon D, Diaz LA Jr, Vogelstein B, Kinzler KW, Velculescu VE, Papadopoulos N (2010) Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 330(6001):228–231. doi:10.1126/science.1196333 CrossRefPubMedPubMedCentral Jones S, Wang TL, Shih Ie M, Mao TL, Nakayama K, Roden R, Glas R, Slamon D, Diaz LA Jr, Vogelstein B, Kinzler KW, Velculescu VE, Papadopoulos N (2010) Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 330(6001):228–231. doi:10.​1126/​science.​1196333 CrossRefPubMedPubMedCentral

go back to reference Robinson DR, Wu YM, Vats P, Su F, Lonigro RJ, Cao X, Kalyana-Sundaram S, Wang R, Ning Y, Hodges L, Gursky A, Siddiqui J, Tomlins SA, Roychowdhury S, Pienta KJ, Kim SY, Roberts JS, Rae JM, Van Poznak CH, Hayes DF, Chugh R, Kunju LP, Talpaz M, Schott AF, Chinnaiyan AM (2013) Activating ESR1 mutations in hormone-resistant metastatic breast cancer. Nat Genet 45(12):1446–1451. doi:10.1038/ng.2823 CrossRefPubMedPubMedCentral Robinson DR, Wu YM, Vats P, Su F, Lonigro RJ, Cao X, Kalyana-Sundaram S, Wang R, Ning Y, Hodges L, Gursky A, Siddiqui J, Tomlins SA, Roychowdhury S, Pienta KJ, Kim SY, Roberts JS, Rae JM, Van Poznak CH, Hayes DF, Chugh R, Kunju LP, Talpaz M, Schott AF, Chinnaiyan AM (2013) Activating ESR1 mutations in hormone-resistant metastatic breast cancer. Nat Genet 45(12):1446–1451. doi:10.​1038/​ng.​2823 CrossRefPubMedPubMedCentral

go back to reference Yan Z, Cui K, Murray DM, Ling C, Xue Y, Gerstein A, Parsons R, Zhao K, Wang W (2005) PBAF chromatin-remodeling complex requires a novel specificity subunit, BAF200, to regulate expression of selective interferon-responsive genes. Genes Dev 19(14):1662–1667. doi:10.1101/gad.1323805 CrossRefPubMedPubMedCentral Yan Z, Cui K, Murray DM, Ling C, Xue Y, Gerstein A, Parsons R, Zhao K, Wang W (2005) PBAF chromatin-remodeling complex requires a novel specificity subunit, BAF200, to regulate expression of selective interferon-responsive genes. Genes Dev 19(14):1662–1667. doi:10.​1101/​gad.​1323805 CrossRefPubMedPubMedCentral

go back to reference Jiao Y, Shi C, Edil BH, de Wilde RF, Klimstra DS, Maitra A, Schulick RD, Tang LH, Wolfgang CL, Choti MA, Velculescu VE, Diaz LA Jr, Vogelstein B, Kinzler KW, Hruban RH, Papadopoulos N (2011) DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors. Science 331(6021):1199–1203. doi:10.1126/science.1200609 CrossRefPubMedPubMedCentral Jiao Y, Shi C, Edil BH, de Wilde RF, Klimstra DS, Maitra A, Schulick RD, Tang LH, Wolfgang CL, Choti MA, Velculescu VE, Diaz LA Jr, Vogelstein B, Kinzler KW, Hruban RH, Papadopoulos N (2011) DAXX/ATRX, MEN1, and mTOR pathway genes are frequently altered in pancreatic neuroendocrine tumors. Science 331(6021):1199–1203. doi:10.​1126/​science.​1200609 CrossRefPubMedPubMedCentral

go back to reference Zekri A, Lesan V, Ghaffari SH, Tabrizi MH, Modarressi MH (2012) Gene amplification and overexpression of Aurora-C in breast and prostate cancer cell lines. Oncol Res 20(5–6):241–250CrossRefPubMed Zekri A, Lesan V, Ghaffari SH, Tabrizi MH, Modarressi MH (2012) Gene amplification and overexpression of Aurora-C in breast and prostate cancer cell lines. Oncol Res 20(5–6):241–250CrossRefPubMed

go back to reference Mobasheri MB, Shirkoohi R, Zendehdel K, Jahanzad I, Talebi S, Afsharpad M, Modarressi MH (2015) Transcriptome analysis of the cancer/testis genes, DAZ1, AURKC, and TEX101, in breast tumors and six breast cancer cell lines. Tumour Biol 36(10):8201–8206. doi:10.1007/s13277-015-3546-4 CrossRefPubMed Mobasheri MB, Shirkoohi R, Zendehdel K, Jahanzad I, Talebi S, Afsharpad M, Modarressi MH (2015) Transcriptome analysis of the cancer/testis genes, DAZ1, AURKC, and TEX101, in breast tumors and six breast cancer cell lines. Tumour Biol 36(10):8201–8206. doi:10.​1007/​s13277-015-3546-4 CrossRefPubMed

go back to reference Nishikawa H, Wu W, Koike A, Kojima R, Gomi H, Fukuda M, Ohta T (2009) BRCA1-associated protein 1 interferes with BRCA1/BARD1 RING heterodimer activity. Cancer Res 69(1):111–119. doi:10.1158/0008-5472.CAN-08-3355 CrossRefPubMed Nishikawa H, Wu W, Koike A, Kojima R, Gomi H, Fukuda M, Ohta T (2009) BRCA1-associated protein 1 interferes with BRCA1/BARD1 RING heterodimer activity. Cancer Res 69(1):111–119. doi:10.​1158/​0008-5472.​CAN-08-3355 CrossRefPubMed

go back to reference Chen X, Arciero CA, Wang C, Broccoli D, Godwin AK (2006) BRCC36 is essential for ionizing radiation-induced BRCA1 phosphorylation and nuclear foci formation. Cancer Res 66(10):5039–5046. doi:10.1158/0008-5472.CAN-05-4194 CrossRefPubMed Chen X, Arciero CA, Wang C, Broccoli D, Godwin AK (2006) BRCC36 is essential for ionizing radiation-induced BRCA1 phosphorylation and nuclear foci formation. Cancer Res 66(10):5039–5046. doi:10.​1158/​0008-5472.​CAN-05-4194 CrossRefPubMed

go back to reference Peng C, Zhou J, Liu HY, Zhou M, Wang LL, Zhang QH, Yang YX, Xiong W, Shen SR, Li XL, Li GY (2006) The transcriptional regulation role of BRD7 by binding to acetylated histone through bromodomain. J Cell Biochem 97(4):882–892. doi:10.1002/jcb.20645 CrossRefPubMed Peng C, Zhou J, Liu HY, Zhou M, Wang LL, Zhang QH, Yang YX, Xiong W, Shen SR, Li XL, Li GY (2006) The transcriptional regulation role of BRD7 by binding to acetylated histone through bromodomain. J Cell Biochem 97(4):882–892. doi:10.​1002/​jcb.​20645 CrossRefPubMed

go back to reference Kim MS, Chung NG, Kang MR, Yoo NJ, Lee SH (2011) Genetic and expressional alterations of CHD genes in gastric and colorectal cancers. Histopathology 58(5):660–668. doi:10.1111/j.1365-2559.2011.03819.x CrossRefPubMed Kim MS, Chung NG, Kang MR, Yoo NJ, Lee SH (2011) Genetic and expressional alterations of CHD genes in gastric and colorectal cancers. Histopathology 58(5):660–668. doi:10.​1111/​j.​1365-2559.​2011.​03819.​x CrossRefPubMed

go back to reference Mullighan CG, Zhang J, Kasper LH, Lerach S, Payne-Turner D, Phillips LA, Heatley SL, Holmfeldt L, Collins-Underwood JR, Ma J, Buetow KH, Pui CH, Baker SD, Brindle PK, Downing JR (2011) CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 471(7337):235–239. doi:10.1038/nature09727 CrossRefPubMedPubMedCentral Mullighan CG, Zhang J, Kasper LH, Lerach S, Payne-Turner D, Phillips LA, Heatley SL, Holmfeldt L, Collins-Underwood JR, Ma J, Buetow KH, Pui CH, Baker SD, Brindle PK, Downing JR (2011) CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 471(7337):235–239. doi:10.​1038/​nature09727 CrossRefPubMedPubMedCentral

go back to reference Ozdag H, Batley SJ, Forsti A, Iyer NG, Daigo Y, Boutell J, Arends MJ, Ponder BA, Kouzarides T, Caldas C (2002) Mutation analysis of CBP and PCAF reveals rare inactivating mutations in cancer cell lines but not in primary tumours. Br J Cancer 87(10):1162–1165. doi:10.1038/sj.bjc.6600554 CrossRefPubMedPubMedCentral Ozdag H, Batley SJ, Forsti A, Iyer NG, Daigo Y, Boutell J, Arends MJ, Ponder BA, Kouzarides T, Caldas C (2002) Mutation analysis of CBP and PCAF reveals rare inactivating mutations in cancer cell lines but not in primary tumours. Br J Cancer 87(10):1162–1165. doi:10.​1038/​sj.​bjc.​6600554 CrossRefPubMedPubMedCentral

go back to reference Schwartzentruber J, Korshunov A, Liu XY, Jones DT, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DA, Tonjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jager N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Fruhwald MC, Roggendorf W, Kramm C, Durken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N (2012) Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature. 482(7384):226–231. doi:10.1038/nature10833 CrossRefPubMed Schwartzentruber J, Korshunov A, Liu XY, Jones DT, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DA, Tonjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jager N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Fruhwald MC, Roggendorf W, Kramm C, Durken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N (2012) Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature. 482(7384):226–231. doi:10.​1038/​nature10833 CrossRefPubMed

go back to reference Chong S, Vickaryous N, Ashe A, Zamudio N, Youngson N, Hemley S, Stopka T, Skoultchi A, Matthews J, Scott HS, de Kretser D, O’Bryan M, Blewitt M, Whitelaw E (2007) Modifiers of epigenetic reprogramming show paternal effects in the mouse. Nat Genet 39(5):614–622. doi:10.1038/ng2031 CrossRefPubMedPubMedCentral Chong S, Vickaryous N, Ashe A, Zamudio N, Youngson N, Hemley S, Stopka T, Skoultchi A, Matthews J, Scott HS, de Kretser D, O’Bryan M, Blewitt M, Whitelaw E (2007) Modifiers of epigenetic reprogramming show paternal effects in the mouse. Nat Genet 39(5):614–622. doi:10.​1038/​ng2031 CrossRefPubMedPubMedCentral

go back to reference Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, Harris CC, Lichti CF, Townsend RR, Fulton RS, Dooling DJ, Koboldt DC, Schmidt H, Zhang Q, Osborne JR, Lin L, O’Laughlin M, McMichael JF, Delehaunty KD, McGrath SD, Fulton LA, Magrini VJ, Vickery TL, Hundal J, Cook LL, Conyers JJ, Swift GW, Reed JP, Alldredge PA, Wylie T, Walker J, Kalicki J, Watson MA, Heath S, Shannon WD, Varghese N, Nagarajan R, Westervelt P, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Wilson RK (2010) DNMT3A mutations in acute myeloid leukemia. N Engl J Med 363(25):2424–2433. doi:10.1056/NEJMoa1005143 CrossRefPubMedPubMedCentral Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, Harris CC, Lichti CF, Townsend RR, Fulton RS, Dooling DJ, Koboldt DC, Schmidt H, Zhang Q, Osborne JR, Lin L, O’Laughlin M, McMichael JF, Delehaunty KD, McGrath SD, Fulton LA, Magrini VJ, Vickery TL, Hundal J, Cook LL, Conyers JJ, Swift GW, Reed JP, Alldredge PA, Wylie T, Walker J, Kalicki J, Watson MA, Heath S, Shannon WD, Varghese N, Nagarajan R, Westervelt P, Tomasson MH, Link DC, Graubert TA, DiPersio JF, Mardis ER, Wilson RK (2010) DNMT3A mutations in acute myeloid leukemia. N Engl J Med 363(25):2424–2433. doi:10.​1056/​NEJMoa1005143 CrossRefPubMedPubMedCentral

go back to reference Yan XJ, Xu J, Gu ZH, Pan CM, Lu G, Shen Y, Shi JY, Zhu YM, Tang L, Zhang XW, Liang WX, Mi JQ, Song HD, Li KQ, Chen Z, Chen SJ (2011) Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat Genet 43(4):309–315. doi:10.1038/ng.788 CrossRefPubMed Yan XJ, Xu J, Gu ZH, Pan CM, Lu G, Shen Y, Shi JY, Zhu YM, Tang L, Zhang XW, Liang WX, Mi JQ, Song HD, Li KQ, Chen Z, Chen SJ (2011) Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat Genet 43(4):309–315. doi:10.​1038/​ng.​788 CrossRefPubMed

go back to reference Bachman KE, Rountree MR, Baylin SB (2001) Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin. J Biol Chem 276(34):32282–32287. doi:10.1074/jbc.M104661200 CrossRefPubMed Bachman KE, Rountree MR, Baylin SB (2001) Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin. J Biol Chem 276(34):32282–32287. doi:10.​1074/​jbc.​M104661200 CrossRefPubMed

go back to reference Bryan EJ, Jokubaitis VJ, Chamberlain NL, Baxter SW, Dawson E, Choong DY, Campbell IG (2002) Mutation analysis of EP300 in colon, breast and ovarian carcinomas. Int J Cancer 102(2):137–141. doi:10.1002/ijc.10682 CrossRefPubMed Bryan EJ, Jokubaitis VJ, Chamberlain NL, Baxter SW, Dawson E, Choong DY, Campbell IG (2002) Mutation analysis of EP300 in colon, breast and ovarian carcinomas. Int J Cancer 102(2):137–141. doi:10.​1002/​ijc.​10682 CrossRefPubMed

go back to reference Ernst T, Chase AJ, Score J, Hidalgo-Curtis CE, Bryant C, Jones AV, Waghorn K, Zoi K, Ross FM, Reiter A, Hochhaus A, Drexler HG, Duncombe A, Cervantes F, Oscier D, Boultwood J, Grand FH, Cross NC (2010) Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders. Nat Genet 42(8):722–726. doi:10.1038/ng.621 CrossRefPubMed Ernst T, Chase AJ, Score J, Hidalgo-Curtis CE, Bryant C, Jones AV, Waghorn K, Zoi K, Ross FM, Reiter A, Hochhaus A, Drexler HG, Duncombe A, Cervantes F, Oscier D, Boultwood J, Grand FH, Cross NC (2010) Inactivating mutations of the histone methyltransferase gene EZH2 in myeloid disorders. Nat Genet 42(8):722–726. doi:10.​1038/​ng.​621 CrossRefPubMed

go back to reference Nikoloski G, Langemeijer SM, Kuiper RP, Knops R, Massop M, Tonnissen ER, van der Heijden A, Scheele TN, Vandenberghe P, de Witte T, van der Reijden BA, Jansen JH (2010) Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes. Nat Genet 42(8):665–667. doi:10.1038/ng.620 CrossRefPubMed Nikoloski G, Langemeijer SM, Kuiper RP, Knops R, Massop M, Tonnissen ER, van der Heijden A, Scheele TN, Vandenberghe P, de Witte T, van der Reijden BA, Jansen JH (2010) Somatic mutations of the histone methyltransferase gene EZH2 in myelodysplastic syndromes. Nat Genet 42(8):665–667. doi:10.​1038/​ng.​620 CrossRefPubMed

go back to reference Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, Paul JE, Boyle M, Woolcock BW, Kuchenbauer F, Yap D, Humphries RK, Griffith OL, Shah S, Zhu H, Kimbara M, Shashkin P, Charlot JF, Tcherpakov M, Corbett R, Tam A, Varhol R, Smailus D, Moksa M, Zhao Y, Delaney A, Qian H, Birol I, Schein J, Moore R, Holt R, Horsman DE, Connors JM, Jones S, Aparicio S, Hirst M, Gascoyne RD, Marra MA (2010) Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet 42(2):181–185. doi:10.1038/ng.518 CrossRefPubMedPubMedCentral Morin RD, Johnson NA, Severson TM, Mungall AJ, An J, Goya R, Paul JE, Boyle M, Woolcock BW, Kuchenbauer F, Yap D, Humphries RK, Griffith OL, Shah S, Zhu H, Kimbara M, Shashkin P, Charlot JF, Tcherpakov M, Corbett R, Tam A, Varhol R, Smailus D, Moksa M, Zhao Y, Delaney A, Qian H, Birol I, Schein J, Moore R, Holt R, Horsman DE, Connors JM, Jones S, Aparicio S, Hirst M, Gascoyne RD, Marra MA (2010) Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet 42(2):181–185. doi:10.​1038/​ng.​518 CrossRefPubMedPubMedCentral

go back to reference Harten SK, Bruxner TJ, Bharti V, Blewitt M, Nguyen TM, Whitelaw E, Epp T (2014) The first mouse mutants of D14Abb1e (Fam208a) show that it is critical for early development. Mamm Genome 25(7–8):293–303. doi:10.1007/s00335-014-9516-0 CrossRefPubMedPubMedCentral Harten SK, Bruxner TJ, Bharti V, Blewitt M, Nguyen TM, Whitelaw E, Epp T (2014) The first mouse mutants of D14Abb1e (Fam208a) show that it is critical for early development. Mamm Genome 25(7–8):293–303. doi:10.​1007/​s00335-014-9516-0 CrossRefPubMedPubMedCentral

go back to reference Roberts AR, Blewitt ME, Youngson NA, Whitelaw E, Chong S (2011) Reduced dosage of the modifiers of epigenetic reprogramming Dnmt1, Dnmt3L, SmcHD1 and Foxo3a has no detectable effect on mouse telomere length in vivo. Chromosoma 120(4):377–385. doi:10.1007/s00412-011-0318-9 CrossRefPubMedPubMedCentral Roberts AR, Blewitt ME, Youngson NA, Whitelaw E, Chong S (2011) Reduced dosage of the modifiers of epigenetic reprogramming Dnmt1, Dnmt3L, SmcHD1 and Foxo3a has no detectable effect on mouse telomere length in vivo. Chromosoma 120(4):377–385. doi:10.​1007/​s00412-011-0318-9 CrossRefPubMedPubMedCentral

go back to reference Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider J, Ballman K, Weber J, Chen K, Koboldt DC, Kandoth C, Schierding WS, McMichael JF, Miller CA, Lu C, Harris CC, McLellan MD, Wendl MC, DeSchryver K, Allred DC, Esserman L, Unzeitig G, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Leitch M, Hunt K, Olson J, Tao Y, Maher CA, Fulton LL, Fulton RS, Harrison M, Oberkfell B, Du F, Demeter R, Vickery TL, Elhammali A, Piwnica-Worms H, McDonald S, Watson M, Dooling DJ, Ota D, Chang LW, Bose R, Ley TJ, Piwnica-Worms D, Stuart JM, Wilson RK, Mardis ER (2012) Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature 486(7403):353–360. doi:10.1038/nature11143 PubMedPubMedCentral Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider J, Ballman K, Weber J, Chen K, Koboldt DC, Kandoth C, Schierding WS, McMichael JF, Miller CA, Lu C, Harris CC, McLellan MD, Wendl MC, DeSchryver K, Allred DC, Esserman L, Unzeitig G, Margenthaler J, Babiera GV, Marcom PK, Guenther JM, Leitch M, Hunt K, Olson J, Tao Y, Maher CA, Fulton LL, Fulton RS, Harrison M, Oberkfell B, Du F, Demeter R, Vickery TL, Elhammali A, Piwnica-Worms H, McDonald S, Watson M, Dooling DJ, Ota D, Chang LW, Bose R, Ley TJ, Piwnica-Worms D, Stuart JM, Wilson RK, Mardis ER (2012) Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature 486(7403):353–360. doi:10.​1038/​nature11143 PubMedPubMedCentral

go back to reference Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B (2007) The genomic landscapes of human breast and colorectal cancers. Science 318(5853):1108–1113. doi:10.1126/science.1145720 CrossRefPubMed Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B (2007) The genomic landscapes of human breast and colorectal cancers. Science 318(5853):1108–1113. doi:10.​1126/​science.​1145720 CrossRefPubMed

go back to reference Figueroa ME, Abdel-Wahab O, Lu C, Ward PS, Patel J, Shih A, Li Y, Bhagwat N, Vasanthakumar A, Fernandez HF, Tallman MS, Sun Z, Wolniak K, Peeters JK, Liu W, Choe SE, Fantin VR, Paietta E, Lowenberg B, Licht JD, Godley LA, Delwel R, Valk PJ, Thompson CB, Levine RL, Melnick A (2010) Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18(6):553–567. doi:10.1016/j.ccr.2010.11.015 CrossRefPubMedPubMedCentral Figueroa ME, Abdel-Wahab O, Lu C, Ward PS, Patel J, Shih A, Li Y, Bhagwat N, Vasanthakumar A, Fernandez HF, Tallman MS, Sun Z, Wolniak K, Peeters JK, Liu W, Choe SE, Fantin VR, Paietta E, Lowenberg B, Licht JD, Godley LA, Delwel R, Valk PJ, Thompson CB, Levine RL, Melnick A (2010) Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell 18(6):553–567. doi:10.​1016/​j.​ccr.​2010.​11.​015 CrossRefPubMedPubMedCentral

go back to reference Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, Davies H, Jones D, Lin ML, Teague J, Bignell G, Butler A, Cho J, Dalgliesh GL, Galappaththige D, Greenman C, Hardy C, Jia M, Latimer C, Lau KW, Marshall J, McLaren S, Menzies A, Mudie L, Stebbings L, Largaespada DA, Wessels LF, Richard S, Kahnoski RJ, Anema J, Tuveson DA, Perez-Mancera PA, Mustonen V, Fischer A, Adams DJ, Rust A, Chan-on W, Subimerb C, Dykema K, Furge K, Campbell PJ, Teh BT, Stratton MR, Futreal PA (2011) Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 469(7331):539–542. doi:10.1038/nature09639 CrossRefPubMedPubMedCentral Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, Davies H, Jones D, Lin ML, Teague J, Bignell G, Butler A, Cho J, Dalgliesh GL, Galappaththige D, Greenman C, Hardy C, Jia M, Latimer C, Lau KW, Marshall J, McLaren S, Menzies A, Mudie L, Stebbings L, Largaespada DA, Wessels LF, Richard S, Kahnoski RJ, Anema J, Tuveson DA, Perez-Mancera PA, Mustonen V, Fischer A, Adams DJ, Rust A, Chan-on W, Subimerb C, Dykema K, Furge K, Campbell PJ, Teh BT, Stratton MR, Futreal PA (2011) Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 469(7331):539–542. doi:10.​1038/​nature09639 CrossRefPubMedPubMedCentral

go back to reference Makinen N, Aavikko M, Heikkinen T, Taipale M, Taipale J, Koivisto-Korander R, Butzow R, Vahteristo P (2016) Exome Sequencing of Uterine Leiomyosarcomas Identifies Frequent Mutations in TP53, ATRX, and MED12. PLoS Genet 12(2):e1005850. doi:10.1371/journal.pgen.1005850 CrossRefPubMedPubMedCentral Makinen N, Aavikko M, Heikkinen T, Taipale M, Taipale J, Koivisto-Korander R, Butzow R, Vahteristo P (2016) Exome Sequencing of Uterine Leiomyosarcomas Identifies Frequent Mutations in TP53, ATRX, and MED12. PLoS Genet 12(2):e1005850. doi:10.​1371/​journal.​pgen.​1005850 CrossRefPubMedPubMedCentral

go back to reference Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder MJ, Yoshiura K, Matsumoto N, Ohta T, Niikawa N, Nickerson DA, Bamshad MJ, Shendure J (2010) Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 42(9):790–793. doi:10.1038/ng.646 CrossRefPubMedPubMedCentral Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder MJ, Yoshiura K, Matsumoto N, Ohta T, Niikawa N, Nickerson DA, Bamshad MJ, Shendure J (2010) Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet 42(9):790–793. doi:10.​1038/​ng.​646 CrossRefPubMedPubMedCentral

go back to reference Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SK, Shinjo SM, Clara C, Phillips PC, Minturn JE, Biegel JA, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Rasheed BA, Friedman HS, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE (2011) The genetic landscape of the childhood cancer medulloblastoma. Science 331(6016):435–439. doi:10.1126/science.1198056 CrossRefPubMed Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SK, Shinjo SM, Clara C, Phillips PC, Minturn JE, Biegel JA, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Rasheed BA, Friedman HS, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE (2011) The genetic landscape of the childhood cancer medulloblastoma. Science 331(6016):435–439. doi:10.​1126/​science.​1198056 CrossRefPubMed

go back to reference Balakrishnan A, Bleeker FE, Lamba S, Rodolfo M, Daniotti M, Scarpa A, van Tilborg AA, Leenstra S, Zanon C, Bardelli A (2007) Novel somatic and germline mutations in cancer candidate genes in glioblastoma, melanoma, and pancreatic carcinoma. Cancer Res 67(8):3545–3550. doi:10.1158/0008-5472.CAN-07-0065 CrossRefPubMed Balakrishnan A, Bleeker FE, Lamba S, Rodolfo M, Daniotti M, Scarpa A, van Tilborg AA, Leenstra S, Zanon C, Bardelli A (2007) Novel somatic and germline mutations in cancer candidate genes in glioblastoma, melanoma, and pancreatic carcinoma. Cancer Res 67(8):3545–3550. doi:10.​1158/​0008-5472.​CAN-07-0065 CrossRefPubMed

go back to reference Li S, Yen L, Pastor WA, Johnston JB, Du J, Shew CJ, Liu W, Ho J, Stender B, Clark AT, Burlingame AL, Daxinger L, Patel DJ, Jacobsen SE (2016) Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin. Proc Natl Acad Sci USA 113(35):E5108–E5116. doi:10.1073/pnas.1609709113 CrossRefPubMedPubMedCentral Li S, Yen L, Pastor WA, Johnston JB, Du J, Shew CJ, Liu W, Ho J, Stender B, Clark AT, Burlingame AL, Daxinger L, Patel DJ, Jacobsen SE (2016) Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin. Proc Natl Acad Sci USA 113(35):E5108–E5116. doi:10.​1073/​pnas.​1609709113 CrossRefPubMedPubMedCentral

go back to reference Desmedt C, Fumagalli D, Pietri E, Zoppoli G, Brown D, Nik-Zainal S, Gundem G, Rothe F, Majjaj S, Garuti A, Carminati E, Loi S, Van Brussel T, Boeckx B, Maetens M, Mudie L, Vincent D, Kheddoumi N, Serra L, Massa I, Ballestrero A, Amadori D, Salgado R, de Wind A, Lambrechts D, Piccart M, Larsimont D, Campbell PJ, Sotiriou C (2015) Uncovering the genomic heterogeneity of multifocal breast cancer. J Pathol 236(4):457–466. doi:10.1002/path.4540 CrossRefPubMedPubMedCentral Desmedt C, Fumagalli D, Pietri E, Zoppoli G, Brown D, Nik-Zainal S, Gundem G, Rothe F, Majjaj S, Garuti A, Carminati E, Loi S, Van Brussel T, Boeckx B, Maetens M, Mudie L, Vincent D, Kheddoumi N, Serra L, Massa I, Ballestrero A, Amadori D, Salgado R, de Wind A, Lambrechts D, Piccart M, Larsimont D, Campbell PJ, Sotiriou C (2015) Uncovering the genomic heterogeneity of multifocal breast cancer. J Pathol 236(4):457–466. doi:10.​1002/​path.​4540 CrossRefPubMedPubMedCentral

go back to reference Wagner BL, Norris JD, Knotts TA, Weigel NL, McDonnell DP (1998) The nuclear corepressors NCoR and SMRT are key regulators of both ligand- and 8-bromo-cyclic AMP-dependent transcriptional activity of the human progesterone receptor. Mol Cell Biol 18(3):1369–1378CrossRefPubMedPubMedCentral Wagner BL, Norris JD, Knotts TA, Weigel NL, McDonnell DP (1998) The nuclear corepressors NCoR and SMRT are key regulators of both ligand- and 8-bromo-cyclic AMP-dependent transcriptional activity of the human progesterone receptor. Mol Cell Biol 18(3):1369–1378CrossRefPubMedPubMedCentral

go back to reference Karhemo PR, Rivinoja A, Lundin J, Hyvonen M, Chernenko A, Lammi J, Sihto H, Lundin M, Heikkila P, Joensuu H, Bono P, Laakkonen P (2011) An extensive tumor array analysis supports tumor suppressive role for nucleophosmin in breast cancer. Am J Pathol 179(2):1004–1014. doi:10.1016/j.ajpath.2011.04.009 CrossRefPubMedPubMedCentral Karhemo PR, Rivinoja A, Lundin J, Hyvonen M, Chernenko A, Lammi J, Sihto H, Lundin M, Heikkila P, Joensuu H, Bono P, Laakkonen P (2011) An extensive tumor array analysis supports tumor suppressive role for nucleophosmin in breast cancer. Am J Pathol 179(2):1004–1014. doi:10.​1016/​j.​ajpath.​2011.​04.​009 CrossRefPubMedPubMedCentral

go back to reference Daxinger L, Harten SK, Oey H, Epp T, Isbel L, Huang E, Whitelaw N, Apedaile A, Sorolla A, Yong J, Bharti V, Sutton J, Ashe A, Pang Z, Wallace N, Gerhardt DJ, Blewitt ME, Jeddeloh JA, Whitelaw E (2013) An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse. Genome Biol 14(9):R96. doi:10.1186/gb-2013-14-9-r96 CrossRefPubMedPubMedCentral Daxinger L, Harten SK, Oey H, Epp T, Isbel L, Huang E, Whitelaw N, Apedaile A, Sorolla A, Yong J, Bharti V, Sutton J, Ashe A, Pang Z, Wallace N, Gerhardt DJ, Blewitt ME, Jeddeloh JA, Whitelaw E (2013) An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse. Genome Biol 14(9):R96. doi:10.​1186/​gb-2013-14-9-r96 CrossRefPubMedPubMedCentral

go back to reference Wu Q, Madany P, Akech J, Dobson JR, Douthwright S, Browne G, Colby JL, Winter GE, Bradner JE, Pratap J, Sluder G, Bhargava R, Chiosea SI, van Wijnen AJ, Stein JL, Stein GS, Lian JB, Nickerson JA, Imbalzano AN (2015) The SWI/SNF ATPases Are Required for Triple Negative Breast Cancer Cell Proliferation. J Cell Physiol 230(11):2683–2694. doi:10.1002/jcp.24991 CrossRefPubMedPubMedCentral Wu Q, Madany P, Akech J, Dobson JR, Douthwright S, Browne G, Colby JL, Winter GE, Bradner JE, Pratap J, Sluder G, Bhargava R, Chiosea SI, van Wijnen AJ, Stein JL, Stein GS, Lian JB, Nickerson JA, Imbalzano AN (2015) The SWI/SNF ATPases Are Required for Triple Negative Breast Cancer Cell Proliferation. J Cell Physiol 230(11):2683–2694. doi:10.​1002/​jcp.​24991 CrossRefPubMedPubMedCentral

go back to reference Rodriguez-Nieto S, Canada A, Pros E, Pinto AI, Torres-Lanzas J, Lopez-Rios F, Sanchez-Verde L, Pisano DG, Sanchez-Cespedes M (2011) Massive parallel DNA pyrosequencing analysis of the tumor suppressor BRG1/SMARCA4 in lung primary tumors. Hum Mutat 32(2):E1999–E2017. doi:10.1002/humu.21415 CrossRefPubMed Rodriguez-Nieto S, Canada A, Pros E, Pinto AI, Torres-Lanzas J, Lopez-Rios F, Sanchez-Verde L, Pisano DG, Sanchez-Cespedes M (2011) Massive parallel DNA pyrosequencing analysis of the tumor suppressor BRG1/SMARCA4 in lung primary tumors. Hum Mutat 32(2):E1999–E2017. doi:10.​1002/​humu.​21415 CrossRefPubMed

go back to reference Bochar DA, Wang L, Beniya H, Kinev A, Xue Y, Lane WS, Wang W, Kashanchi F, Shiekhattar R (2000) BRCA1 is associated with a human SWI/SNF-related complex: linking chromatin remodeling to breast cancer. Cell 102(2):257–265CrossRefPubMed Bochar DA, Wang L, Beniya H, Kinev A, Xue Y, Lane WS, Wang W, Kashanchi F, Shiekhattar R (2000) BRCA1 is associated with a human SWI/SNF-related complex: linking chromatin remodeling to breast cancer. Cell 102(2):257–265CrossRefPubMed

go back to reference Ring HZ, Vameghi-Meyers V, Wang W, Crabtree GR, Francke U (1998) Five SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin (SMARC) genes are dispersed in the human genome. Genomics 51(1):140–143. doi:10.1006/geno.1998.5343 CrossRefPubMed Ring HZ, Vameghi-Meyers V, Wang W, Crabtree GR, Francke U (1998) Five SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin (SMARC) genes are dispersed in the human genome. Genomics 51(1):140–143. doi:10.​1006/​geno.​1998.​5343 CrossRefPubMed

go back to reference Legare S, Cavallone L, Mamo A, Chabot C, Sirois I, Magliocco A, Klimowicz A, Tonin PN, Buchanan M, Keilty D, Hassan S, Laperriere D, Mader S, Aleynikova O, Basik M (2015) The estrogen receptor cofactor SPEN functions as a tumor suppressor and candidate biomarker of drug responsiveness in hormone-dependent breast cancers. Cancer Res 75(20):4351–4363. doi:10.1158/0008-5472.CAN-14-3475 CrossRefPubMed Legare S, Cavallone L, Mamo A, Chabot C, Sirois I, Magliocco A, Klimowicz A, Tonin PN, Buchanan M, Keilty D, Hassan S, Laperriere D, Mader S, Aleynikova O, Basik M (2015) The estrogen receptor cofactor SPEN functions as a tumor suppressor and candidate biomarker of drug responsiveness in hormone-dependent breast cancers. Cancer Res 75(20):4351–4363. doi:10.​1158/​0008-5472.​CAN-14-3475 CrossRefPubMed

go back to reference Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324(5929):930–935. doi:10.1126/science.1170116 CrossRefPubMedPubMedCentral Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu DR, Aravind L, Rao A (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324(5929):930–935. doi:10.​1126/​science.​1170116 CrossRefPubMedPubMedCentral

go back to reference Ito S, D’Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y (2010) Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466(7310):1129–1133. doi:10.1038/nature09303 CrossRefPubMedPubMedCentral Ito S, D’Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y (2010) Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466(7310):1129–1133. doi:10.​1038/​nature09303 CrossRefPubMedPubMedCentral