DNA methylation profiling to assess pathogenicity of BRCA1 unclassified variants in breast cancer

References

• Ferlay J, Shin HR, Bray F, Forman D, Mathers C, Parkin DM. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer 2010; 127:2893–917; PMID:21351269; http://dx.doi.org/10.1002/ijc.25516
   PubMed Web of Science ®Google Scholar
• TCGA. Comprehensive molecular portraits of human breast tumours. Nature 2012; 490:61–70; PMID:23000897; http://dx.doi.org/10.1038/nature11412
   PubMed Web of Science ®Google Scholar
• Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, et al. The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 2012; 486:346–52; PMID:22522925; http://dx.doi:10.1038/nature10983
   PubMed Web of Science ®Google Scholar
• Smith P, McGuffog L, Easton DF, Mann GJ, Pupo GM, Newman B, Chenevix-Trench G, Szabo C, Southey M, Renard H, et al. A genome wide linkage search for breast cancer susceptibility genes. Genes Chromosomes Cancer 2006; 45:646–55; PMID:16575876; http://dx.doi.org/10.1002/gcc.20354
   PubMed Web of Science ®Google Scholar
• Eggington JM, Bowles KR, Moyes K, Manley S, Esterling L, Sizemore S, Rosenthal E, Theisen A, Saam J, Arnell C, et al. A comprehensive laboratory-based program for classification of variants of uncertain significance in hereditary cancer genes. Clin Genet 2014; 86:229–37; PMID:24304220; http://dx.doi.org/10.1111/cge.12315
   PubMed Web of Science ®Google Scholar
• Lindor NM, Goldgar DE, Tavtigian SV, Plon SE, Couch FJ. BRCA1/2 sequence variants of uncertain significance: a primer for providers to assist in discussions and in medical management. Oncologist 2013; 18:518–24; PMID:23615697; http://dx.doi.org/10.1634/theoncologist.2012-0452
   PubMed Web of Science ®Google Scholar
• Easton DF, Deffenbaugh AM, Pruss D, Frye C, Wenstrup RJ, Allen-Brady K, Tavtigian SV, Monteiro AN, Iversen ES, Couch FJ, et al. A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes. Am J Hum Genet 2007; 81:873–83; PMID:17924331; http://dx.doi.org/10.1086/521032
   PubMed Web of Science ®Google Scholar
• Goldgar DE, Easton DF, Byrnes GB, Spurdle AB, Iversen ES, Greenblatt MS. Genetic evidence and integration of various data sources for classifying uncertain variants into a single model. Hum Mutat 2008; 29:1265–72; PMID:18951437; http://dx.doi.org/10.1002/humu.20897
   PubMed Web of Science ®Google Scholar
• Tavtigian SV, Byrnes GB, Goldgar DE, Thomas A. Classification of rare missense substitutions, using risk surfaces, with genetic- and molecular-epidemiology applications. Hum Mutat 2008; 29:1342–54; PMID:18951461; http://dx.doi.org/10.1002/humu.20896
   PubMed Web of Science ®Google Scholar
• Spurdle AB, Couch FJ, Hogervorst FB, Radice P, Sinilnikova OM. Prediction and assessment of splicing alterations: implications for clinical testing. Hum Mutat 2008; 29:1304–13; PMID:18951448; http://dx.doi.org/10.1002/humu.20901
   PubMed Web of Science ®Google Scholar
• Tavtigian SV, Greenblatt MS, Goldgar DE, Boffetta P. Assessing pathogenicity: overview of results from the IARC Unclassified Genetic Variants Working Group. Hum Mutat 2008; 29:1261–4; PMID:18951436; http://dx.doi.org/10.1002/humu.20903
   PubMed Web of Science ®Google Scholar
• Plon SE, Eccles DM, Easton D, Foulkes WD, Genuardi M, Greenblatt MS, Hogervorst FB, Hoogerbrugge N, Spurdle AB, Tavtigian SV. Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results. Hum Mutat 2008; 29:1282–91; PMID:18951446; http://dx.doi.org/10.1002/humu.20880
   PubMed Web of Science ®Google Scholar
• Flanagan JM, Cocciardi S, Waddell N, Johnstone CN, Marsh A, Henderson S, Simpson P, da Silva L, Khanna K, Lakhani S, et al. DNA methylome of familial breast cancer identifies distinct profiles defined by mutation status. Am J Hum Genet 2010; 86:420–33; PMID:20206335; http://dx.doi.org/10.1016/j.ajhg.2010.02.008
   PubMed Web of Science ®Google Scholar
• Holm K, Hegardt C, Staaf J, Vallon-Christersson J, Jonsson G, Olsson H, Borg A, Ringner M. Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. Breast Cancer Res 2010; 12:R36; PMID:20565864; http://dx.doi.org/10.1186/bcr2590
   PubMed Web of Science ®Google Scholar
• Spurdle AB, Couch FJ, Parsons MT, McGuffog L, Barrowdale D, Bolla MK, Wang Q, Healey S, Schmutzler RK, Wappenschmidt B, et al. Refined histopathological predictors of BRCA1 and BRCA2 mutation status: a large-scale analysis of breast cancer characteristics from the BCAC, CIMBA, and ENIGMA consortia. Breast Cancer Res 2014; 16:3419: In Press; http://dx.doi.org/10.1186/s13058-014-0474-y
   PubMed Web of Science ®Google Scholar
• Thirlwell C, Eymard M, Feber A, Teschendorff A, Pearce K, Lechner M, Widschwendter M, Beck S. Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium HumanMethylation27 BeadChip. Methods 2010; 52:248–54; PMID:20434562; http://dx.doi.org/10.1016/j.ymeth.2010.04.012
   PubMed Web of Science ®Google Scholar
• Spurdle AB, Whiley PJ, Thompson B, Feng B, Healey S, Brown MA, Pettigrew C, Van Asperen CJ, Ausems MG, Kattentidt-Mouravieva AA, et al. BRCA1 R1699Q variant displaying ambiguous functional abrogation confers intermediate breast and ovarian cancer risk. J Med Genet 2012; 49:525–32; PMID:22889855; http://dx.doi.org/10.1136/jmedgenet-2012-101037
   PubMed Web of Science ®Google Scholar
• Bediaga NG, Acha-Sagredo A, Guerra I, Viguri A, Albaina C, Ruiz Diaz I, Rezola R, Alberdi MJ, Dopazo J, Montaner D, et al. DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Res 2010; 12:R77; PMID:20920229; http://dx.doi.org/10.1186/bcr2721
   PubMed Web of Science ®Google Scholar
• Van der Auwera I, Yu W, Suo L, Van Neste L, van Dam P, Van Marck EA, Pauwels P, Vermeulen PB, Dirix LY, Van Laere SJ. Array-based DNA methylation profiling for breast cancer subtype discrimination. PLoS One 2010; 5:e12616; PMID:20830311; http://dx.doi.org/10.1371/journal.pone.0012616
   PubMed Web of Science ®Google Scholar
• Ronneberg JA, Fleischer T, Solvang HK, Nordgard SH, Edvardsen H, Potapenko I, Nebdal D, Daviaud C, Gut I, Bukholm I, et al. Methylation profiling with a panel of cancer related genes: association with estrogen receptor, TP53 mutation status and expression subtypes in sporadic breast cancer. Mol Oncol 2011; 5:61–76; PMID:21212030; http://dx.doi.org/10.1016/j.molonc.2010.11.004
   PubMed Web of Science ®Google Scholar
• Kamalakaran S, Varadan V, Giercksky Russnes HE, Levy D, Kendall J, Janevski A, Riggs M, Banerjee N, Synnestvedt M, Schlichting E, et al. DNA methylation patterns in luminal breast cancers differ from non-luminal subtypes and can identify relapse risk independent of other clinical variables. Mol Oncol 2011; 5:77–92; PMID:21169070; http://dx.doi.org/10.1016/j.molonc.2010.11.002
   PubMed Web of Science ®Google Scholar
• Killian JK, Bilke S, Davis S, Walker RL, Jaeger E, Killian MS, Waterfall JJ, Bibikova M, Fan JB, Smith WI, Jr, et al. A methyl-deviator epigenotype of estrogen receptor-positive breast carcinoma is associated with malignant biology. Am J Pathol 2011; 179:55–65; PMID:21641572; http://dx.doi.org/10.1016/j.ajpath.2011.03.022
   PubMed Web of Science ®Google Scholar
• Dedeurwaerder S, Desmedt C, Calonne E, Singhal SK, Haibe-Kains B, Defrance M, Michiels S, Volkmar M, Deplus R, Luciani J, et al. DNA methylation profiling reveals a predominant immune component in breast cancers. EMBO Mol Med 2011; 3:726–41; PMID:21910250; http://dx.doi.org/10.1002/emmm.201100801
   PubMed Web of Science ®Google Scholar
• Fackler MJ, Umbricht CB, Williams D, Argani P, Cruz LA, Merino VF, Teo WW, Zhang Z, Huang P, Visvananthan K, et al. Genome-wide methylation analysis identifies genes specific to breast cancer hormone receptor status and risk of recurrence. Cancer Res 2011; 71:6195–207; PMID:21825015; http://dx.doi.org/10.1158/0008-5472.CAN-11-1630
   PubMed Web of Science ®Google Scholar
• Lovelock PK, Spurdle AB, Mok MT, Farrugia DJ, Lakhani SR, Healey S, Arnold S, Buchanan D, Couch FJ, Henderson BR, et al. Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants? Breast Cancer Res 2007; 9:R82; PMID:18036263; http://dx.doi.org/10.1186/bcr1826
   PubMed Web of Science ®Google Scholar
• Gomez Garcia EB, Oosterwijk JC, Timmermans M, van Asperen CJ, Hogervorst FB, Hoogerbrugge N, Oldenburg R, Verhoef S, Dommering CJ, Ausems MG, et al. A method to assess the clinical significance of unclassified variants in the BRCA1 and BRCA2 genes based on cancer family history. Breast Cancer Res 2009; 11:R8; PMID:19200354; http://dx.doi.org/10.1186/bcr2223
   PubMed Web of Science ®Google Scholar
• Clapperton JA, Manke IA, Lowery DM, Ho T, Haire LF, Yaffe MB, Smerdon SJ. Structure and mechanism of BRCA1 BRCT domain recognition of phosphorylated BACH1 with implications for cancer. Nat Struct Mol Biol 2004; 11:512–8; PMID:15133502; http://dx.doi.org/10.1038/nsmb775
   PubMed Web of Science ®Google Scholar
• Bouwman P, van der Gulden H, van der Heijden I, Drost R, Klijn CN, Prasetyanti P, Pieterse M, Wientjens E, Seibler J, Hogervorst FB, et al. A high-throughput functional complementation assay for classification of BRCA1 missense variants. Cancer Discov 2013; 3:1142–55; PMID:23867111; http://dx.doi.org/10.1158/2159-8290.CD-13-0094
   PubMed Web of Science ®Google Scholar
• Tung N, Wang Y, Collins LC, Kaplan J, Li H, Gelman R, Comander AH, Gallagher B, Fetten K, Krag K, et al. Estrogen receptor positive breast cancers in BRCA1 mutation carriers: clinical risk factors and pathologic features. Breast Cancer Res 2010; 12:R12; PMID:20149218; http://dx.doi.org/10.1186/bcr2478
   PubMed Web of Science ®Google Scholar
• Natrajan R, Mackay A, Lambros MB, Weigelt B, Wilkerson PM, Manie E, Grigoriadis A, A'Hern R, van der Groep P, Kozarewa I, et al. A whole-genome massively parallel sequencing analysis of BRCA1 mutant oestrogen receptor-negative and -positive breast cancers. J Pathol 2012; 227:29–41; PMID:22362584; http://dx.doi.org/10.1002/path.4003
   PubMed Web of Science ®Google Scholar
• Oyama T, Ishikawa Y, Hayashi M, Arihiro K, Horiguchi J. The effects of fixation, processing and evaluation criteria on immunohistochemical detection of hormone receptors in breast cancer. Breast Cancer 2007; 14:182–8; PMID:17485904; http://dx.doi.org/10.2325/jbcs.976
   PubMedGoogle Scholar
• Marinsek ZP, Nolde N, Kardum-Skelin I, Nizzoli R, Onal B, Rezanko T, Tani E, Ostovic KT, Vielh P, Schmitt F, et al. Multinational study of oestrogen and progesterone receptor immunocytochemistry on breast carcinoma fine needle aspirates. Cytopathology 2013; 24:7–20; PMID:23082931; http://dx.doi.org/10.1111/cyt.12024
   PubMed Web of Science ®Google Scholar
• Wells CA, Sloane JP, Coleman D, Munt C, Amendoeira I, Apostolikas N, Bellocq JP, Bianchi S, Boecker W, Bussolati G, et al. Consistency of staining and reporting of oestrogen receptor immunocytochemistry within the European Union–an inter-laboratory study. Virchows Arch 2004; 445:119–28; PMID:15221370; http://dx.doi.org/10.1007/s00428-004-1063-8
   PubMed Web of Science ®Google Scholar
• Mann GJ, Thorne H, Balleine RL, Butow PN, Clarke CL, Edkins E, Evans GM, Fereday S, Haan E, Gattas M, et al. Analysis of cancer risk and BRCA1 and BRCA2 mutation prevalence in the kConFab familial breast cancer resource. Breast Cancer Res 2006; 8:R12; PMID:16507150; http://dx.doi.org/10.1186/bcr1377
   PubMed Web of Science ®Google Scholar
• Royo JL, Hidalgo M, Ruiz A. Pyrosequencing protocol using a universal biotinylated primer for mutation detection and SNP genotyping. Nat Protoc 2007; 2:1734–9; PMID:17641638; http://dx.doi.org/10.1038/nprot.2007.244
   PubMed Web of Science ®Google Scholar
• van Beers EH, Joosse SA, Ligtenberg MJ, Fles R, Hogervorst FB, Verhoef S, Nederlof PM. A multiplex PCR predictor for aCGH success of FFPE samples. Br J Cancer 2006; 94:333–7; PMID:16333309; http://dx.doi.org/10.1038/sj.bjc.6602889
   PubMed Web of Science ®Google Scholar
• Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007; 8:118–27; PMID:16632515; http://dx.doi.org/10.1093/biostatistics/kxj037
   PubMed Web of Science ®Google Scholar
• Whiley PJ, Parsons MT, Leary J, Tucker K, Warwick L, Dopita B, Thorne H, Lakhani SR, Goldgar DE, Brown MA, et al. Multifactorial likelihood assessment of BRCA1 and BRCA2 missense variants confirms that BRCA1:c.122A>G(p.His41Arg) is a pathogenic mutation. PLoS One 2014; 9:e86836; PMID:24489791; http://dx.doi.org/10.1371/journal.pone.0086836
   PubMed Web of Science ®Google Scholar
• Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol 2004; 11:377–94; PMID:15285897; http://dx.doi.org/10.1089/1066527041410418
   PubMed Web of Science ®Google Scholar