Erratum: Genomic profiling of breast tumours in relation to BRCAabnormalities and phenotypes [Breast Cancer Research 11, (2009)(R47)] DOI: 10.1186/bcr2334;Genomic profiling of breast tumours in relation to BRCA abnormalities and phenotypes

Breast Cancer Research

Volumn 11, Issue 4, 2009, Pages

  Stefansson, Olafur A ^a   Jonasson, Jon G ^b   Johannsson, Oskar T ^b   Olafsdottir, Kristrun ^b   Steinarsdottir, Margret ^b   Valgeirsdottir, Sigridur ^c   Eyfjord, Jorunn E ^a  

^a UNIVERSITY OF ICELAND   (Iceland)

^b LANDSPITALI UNIVERSITY HOSPITAL   (Iceland)

^c Roche NimbleGen Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN; CYTOKERATIN 18; CYTOKERATIN 5; CYTOKERATIN 6; CYTOKERATIN 8; DNA; EPIDERMAL GROWTH FACTOR RECEPTOR; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; PROGESTERONE RECEPTOR; TUMOR MARKER;

ADULT; ARTICLE; BREAST TUMOR; COMPARATIVE GENOMIC HYBRIDIZATION; FEMALE; GENE DELETION; GENE EXPRESSION PROFILING; GENOMIC INSTABILITY; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; MAJOR CLINICAL STUDY; MICROARRAY ANALYSIS; PHENOTYPE; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; DNA MICROARRAY; GENE DOSAGE; GENETICS; GENOTYPE; PATHOLOGY; TUMOR SUPPRESSOR GENE;

BREAST NEOPLASMS; CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; FEMALE; GENE DOSAGE; GENE EXPRESSION PROFILING; GENES, BRCA1; GENES, BRCA2; GENOMIC INSTABILITY; GENOTYPE; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; SEQUENCE DELETION; TUMOR MARKERS, BIOLOGICAL;

EID: 77149179427     PISSN: 14655411     EISSN: 1465542X     Source Type: Journal    
DOI: 10.1186/bcr2355     Document Type: Erratum

References (47)

1. Fackenthal JD, Olopade OI. Breast cancer risk associated with BRCA1 and BRCA2 in diverse populations. Nat Rev Cancer 2007, 7:937-948. 10.1038/nrc2054, 18034184.
2. Collins N, McManus R, Wooster R, Mangion J, Seal S, Lakhani SR, Ormiston W, Daly PA, Ford D, Easton DF. Consistent loss of the wild type allele in breast cancers from a family linked to the BRCA2 gene on chromosome 13q12-13. Oncogene 1995, 10:1673-1675.
3. Smith SA, Easton DF, Evans DG, Ponder BA. Allele losses in the region 17q12-21 in familial breast and ovarian cancer involve the wild-type chromosome. Nat Genet 1992, 2:128-131. 10.1038/ng1092-128, 1303261.
4. Gudmundsdottir K, Ashworth A. The roles of BRCA1 and BRCA2 and associated proteins in the maintenance of genomic stability. Oncogene 2006, 25:5864-5874. 10.1038/sj.onc.1209874, 16998501.
5. Matsuoka S, Ballif BA, Smogorzewska A, McDonald ER, Hurov KE, Luo J, Bakalarski CE, Zhao Z, Solimini N, Lerenthal Y, Shiloh Y, Gygi SP, Elledge SJ. ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage. Science 2007, 316:1160-1166. 10.1126/science.1140321, 17525332.
6. Greenberg RA, Sobhian B, Pathania S, Cantor SB, Nakatani Y, Livingston DM. Multifactorial contributions to an acute DNA damage response by BRCA1/BARD1-containing complexes. Genes Dev 2006, 20:34-46. 1356099, 16391231, 10.1101/gad.1381306.
7. Yang H, Li Q, Fan J, Holloman WK, Pavletich NP. The BRCA2 homologue Brh2 nucleates RAD51 filament formation at a dsDNA-ssDNA junction. Nature 2005, 433:653-657. 10.1038/nature03234, 15703751.
8. Wang W. Emergence of a DNA-damage response network consisting of Fanconi anaemia and BRCA proteins. Nat Rev Genet 2007, 8:735-748. 10.1038/nrg2159, 17768402.
9. Martin SA, Lord CJ, Ashworth A. DNA repair deficiency as a therapeutic target in cancer. Curr Opin Genet Dev 2008, 18:80-86. 10.1016/j.gde.2008.01.016, 18343102.
10. Futreal PA, Liu Q, Shattuck-Eidens D, Cochran C, Harshman K, Tavtigian S, Bennett LM, Haugen-Strano A, Swensen J, Miki Y. BRCA1 mutations in primary breast and ovarian carcinomas. Science 1994, 266:120-122. 10.1126/science.7939630, 7939630.
11. Lancaster JM, Wooster R, Mangion J, Phelan CM, Cochran C, Gumbs C, Seal S, Barfoot R, Collins N, Bignell G, Patel S, Hamoudi R, Larsson C, Wiseman RW, Berchuck A, Iglehart JD, Marks JR, Ashworth A, Stratton MR, Futreal PA. BRCA2 mutations in primary breast and ovarian cancers. Nat Genet 1996, 13:238-240. 10.1038/ng0696-238, 8640235.
12. Wei M, Grushko TA, Dignam J, Hagos F, Nanda R, Sveen L, Xu J, Fackenthal J, Tretiakova M, Das S, Olopade OI. BRCA1 promoter methylation in sporadic breast cancer is associated with reduced BRCA1 copy number and chromosome 17 aneusomy. Cancer Res 2005, 65:10692-10699. 10.1158/0008-5472.CAN-05-1277, 16322213.
13. Birgisdottir V, Stefansson OA, Bodvarsdottir SK, Hilmarsdottir H, Jonasson JG, Eyfjord JE. Epigenetic silencing and deletion of the BRCA1 gene in sporadic breast cancer. Breast Cancer Res 2006, 8:R38. 1779478, 16846527, 10.1186/bcr1522.
14. Hughes-Davies L, Huntsman D, Ruas M, Fuks F, Bye J, Chin SF, Milner J, Brown LA, Hsu F, Gilks B, Nielsen T, Schulzer M, Chia S, Ragaz J, Cahn A, Linger L, Ozdag H, Cattaneo E, Jordanova ES, Schuuring E, Yu DS, Venkitaraman A, Ponder B, Doherty A, Aparicio S, Bentley D, Theillet C, Ponting CP, Caldas C, Kouzarides T. EMSY links the BRCA2 pathway to sporadic breast and ovarian cancer. Cell 2003, 115:523-535. 10.1016/S0092-8674(03)00930-9, 14651845.
15. Perou CM, Sorlie T, Eisen MB, Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lonning PE, Borresen-Dale AL, Brown PO, Botstein D. Molecular portraits of human breast tumours. Nature 2000, 406:747-752. 10.1038/35021093, 10963602.
16. Chin K, DeVries S, Fridlyand J, Spellman PT, Roydasgupta R, Kuo WL, Lapuk A, Neve RM, Qian Z, Ryder T, Chen F, Feiler H, Tokuyasu T, Kingsley C, Dairkee S, Meng Z, Chew K, Pinkel D, Jain A, Ljung BM, Esserman L, Albertson DG, Waldman FM, Gray JW. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell 2006, 10:529-541. 10.1016/j.ccr.2006.10.009, 17157792.
17. van't Veer LJ, Dai H, Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH. Gene expression profiling predicts clinical outcome of breast cancer. Nature 2002, 415:530-536. 10.1038/415530a, 11823860.
18. Turner NC, Reis-Filho JS, Russell AM, Springall RJ, Ryder K, Steele D, Savage K, Gillett CE, Schmitt FC, Ashworth A, Tutt AN. BRCA1 dysfunction in sporadic basal-like breast cancer. Oncogene 2007, 26:2126-2132. 10.1038/sj.onc.1210014, 17016441.
19. Bergamaschi A, Kim YH, Wang P, Sorlie T, Hernandez-Boussard T, Lonning PE, Tibshirani R, Borresen-Dale AL, Pollack JR. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 2006, 45:1033-1040. 10.1002/gcc.20366, 16897746.
20. Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa JL, Pinder SE, Wiel MA, Green AR, Ellis IO, Porter PL, Tavare S, Brenton JD, Ylstra B, Caldas C. High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol 2007, 8:R215. 2246289, 17925008, 10.1186/gb-2007-8-10-r215.
21. Thorlacius S, Olafsdottir G, Tryggvadottir L, Neuhausen S, Jonasson JG, Tavtigian SV, Tulinius H, Ogmundsdottir HM, Eyfjord JE. A single BRCA2 mutation in male and female breast cancer families from Iceland with varied cancer phenotypes. Nat Genet 1996, 13:117-119. 10.1038/ng0596-117, 8673089.
22. Bergthorsson JT, Jonasdottir A, Johannesdottir G, Arason A, Egilsson V, Gayther S, Borg A, Hakanson S, Ingvarsson S, Barkardottir RB. Identification of a novel splice-site mutation of the BRCA1 gene in two breast cancer families: screening reveals low frequency in Icelandic breast cancer patients. Hum Mutat 1998, (Suppl 1):S195-197.
23. Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, Nair P, Brothman AR, Stallings RL. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 2005, 44:305-319. 10.1002/gcc.20243, 16075461.
24. Gentleman R, Carey VJ, Huber W, Irizarry R, Dudoit S. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5:R80. 545600, 15461798, 10.1186/gb-2004-5-10-r80.
25. Cheang MC, Voduc D, Bajdik C, Leung S, McKinney S, Chia SK, Perou CM, Nielsen TO. Basal-like breast cancer defined by five biomarkers has superior prognostic value than triple-negative phenotype. Clin Cancer Res 2008, 14:1368-1376. 10.1158/1078-0432.CCR-07-1658, 18316557.
26. Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 2004, 5:557-572. 10.1093/biostatistics/kxh008, 15475419.
27. Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 2006, 6:96. 1459181, 16620391, 10.1186/1471-2407-6-96.
28. Pollack JR, Sorlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Borresen-Dale AL, Brown PO. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci USA 2002, 99:12963-12968. 130569, 12297621, 10.1073/pnas.162471999.
29. Hosack DA, Dennis G, Sherman BT, Lane HC, Lempicki RA. Identifying biological themes within lists of genes with EASE. Genome Biol 2003, 4:R70. 328459, 14519205, 10.1186/gb-2003-4-10-r70.
30. Fridlyand J, Snijders AM, Ylstra B, Li H, Olshen A, Segraves R, Dairkee S, Tokuyasu T, Ljung BM, Jain AN, McLennan J, Ziegler J, Chin K, Devries S, Feiler H, Gray JW, Waldman F, Pinkel D, Albertson DG. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 2006, 6:96. 1459181, 16620391, 10.1186/1471-2407-6-96.
31. Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, Leibu E, Esposito D, Alexander J, Troge J, Grubor V, Yoon S, Wigler M, Ye K, Borresen-Dale AL, Naume B, Schlicting E, Norton L, Hagerstrom T, Skoog L, Auer G, Maner S, Lundin P, Zetterberg A. Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res 2006, 16:1465-1479. 1665631, 17142309, 10.1101/gr.5460106.
32. Snouwaert JN, Gowen LC, Latour AM, Mohn AR, Xiao A, DiBiase L, Koller BH. BRCA1 deficient embryonic stem cells display a decreased homologous recombination frequency and an increased frequency of non-homologous recombination that is corrected by expression of a brca1 transgene. Oncogene 1999, 18:7900-7907. 10.1038/sj.onc.1203334, 10630642.
33. Tutt A, Bertwistle D, Valentine J, Gabriel A, Swift S, Ross G, Griffin C, Thacker J, Ashworth A. Mutation in Brca2 stimulates error-prone homology-directed repair of DNA double-strand breaks occurring between repeated sequences. EMBO J 2001, 20:4704-4716. 125603, 11532935, 10.1093/emboj/20.17.4704.
34. Eyfjord JE, Bodvarsdottir SK. Genomic instability and cancer: networks involved in response to DNA damage. Mutat Res 2005, 592:18-28.
35. Ayouaz A, Raynaud C, Heride C, Revaud D, Sabatier L. Telomeres: hallmarks of radiosensitivity. Biochimie 2008, 90:60-72. 10.1016/j.biochi.2007.09.011, 18006207.
36. Jonsson G, Naylor TL, Vallon-Christersson J, Staaf J, Huang J, Ward MR, Greshock JD, Luts L, Olsson H, Rahman N, Stratton M, Ringner M, Borg A, Weber BL. Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization. Cancer Res 2005, 65:7612-7621.
37. van Beers EH, van Welsem T, Wessels LF, Li Y, Oldenburg RA, Devilee P, Cornelisse CJ, Verhoef S, Hogervorst FB, van't Veer LJ, Nederlof PM. Comparative genomic hybridization profiles in human BRCA1 and BRCA2 breast tumors highlight differential sets of genomic aberrations. Cancer Res 2005, 65:822-827.
38. Tirkkonen M, Johannsson O, Agnarsson BA, Olsson H, Ingvarsson S, Karhu R, Tanner M, Isola J, Barkardottir RB, Borg A, Kallioniemi OP. Distinct somatic genetic changes associated with tumor progression in carriers of BRCA1 and BRCA2 germ-line mutations. Cancer Res 1997, 57:1222-1227.
39. Foulkes WD, Stefansson IM, Chappuis PO, Begin LR, Goffin JR, Wong N, Trudel M, Akslen LA. Germline BRCA1 mutations and a basal epithelial phenotype in breast cancer. J Natl Cancer Inst 2003, 95:1482-1485.
40. Bane AL, Beck JC, Bleiweiss I, Buys SS, Catalano E, Daly MB, Giles G, Godwin AK, Hibshoosh H, Hopper JL, John EM, Layfield L, Longacre T, Miron A, Senie R, Southey MC, West DW, Whittemore AS, Wu H, Andrulis IL, O'Malley FP. BRCA2 mutation-associated breast cancers exhibit a distinguishing phenotype based on morphology and molecular profiles from tissue microarrays. Am J Surg Pathol 2007, 31:121-128. 10.1097/01.pas.0000213351.49767.0f, 17197928.
41. King TA, Li W, Brogi E, Yee CJ, Gemignani ML, Olvera N, Levine DA, Norton L, Robson ME, Offit K, Borgen PI, Boyd J. Heterogenic loss of the wild-type BRCA allele in human breast tumorigenesis. Ann Surg Oncol 2007, 14:2510-2518. 10.1245/s10434-007-9372-1, 17597348.
42. Warren M, Lord CJ, Masabanda J, Griffin D, Ashworth A. Phenotypic effects of heterozygosity for a BRCA2 mutation. Hum Mol Genet 2003, 12:2645-2656. 10.1093/hmg/ddg277, 12928478.
43. Kote-Jarai Z, Matthews L, Osorio A, Shanley S, Giddings I, Moreews F, Locke I, Evans DG, Eccles D, , Williams RD, Girolami M, Campbell C, Eeles R. Carrier Clinic Collaborators Accurate prediction of BRCA1 and BRCA2 heterozygous genotype using expression profiling after induced DNA damage. Clin Cancer Res 2006, 12:3896-3901. 10.1158/1078-0432.CCR-05-2805, 16818684, Carrier Clinic Collaborators.
44. Melchor L, Honrado E, Huang J, Alvarez S, Naylor TL, Garcia MJ, Osorio A, Blesa D, Stratton MR, Weber BL, Cigudosa JC, Rahman N, Nathanson KL, Benitez J. Estrogen receptor status could modulate the genomic pattern in familial and sporadic breast cancer. Clin Cancer Res 2007, 13:7305-7313. 10.1158/1078-0432.CCR-07-0711, 18094411.
45. Herschkowitz JI, Simin K, Weigman VJ, Mikaelian I, Usary J, Hu Z, Rasmussen KE, Jones LP, Assefnia S, Chandrasekharan S, Backlund MG, Yin Y, Khramtsov AI, Bastein R, Quackenbush J, Glazer RI, Brown PH, Green JE, Kopelovich L, Furth PA, Palazzo JP, Olopade OI, Bernard PS, Churchill GA, Van Dyke T, Perou CM. Identification of conserved gene expression features between murine mammary carcinoma models and human breast tumors. Genome Biol 2007, 8:R76. 1929138, 17493263, 10.1186/gb-2007-8-5-r76.
46. Fong PC, Boss DS, Yap TA, Tutt A, Wu P, Mergui-Roelvink M, Mortimer P, Swaisland H, Lau A, O'Connor MJ, Ashworth A, Carmichael J, Kaye SB, Schellens JH, de Bono JS. Inhibition of poly(ADP-ribose) polymerase in tumors from BRCA mutation carriers. N Engl J Med 2009, 361:123-134. 10.1056/NEJMoa0900212, 19553641.
47. Moule R, Sohaib A, Eeles R. Dramatic Response to Platinum in a Patient with Cancer with a Germline BRCA2 Mutation. Clin Oncol (R Coll Radiol) 2009, 21:444-447.