Prediction of BRCA2-association in hereditary breast carcinomas using array-CGH

Breast Cancer Research and Treatment

Volumn 132, Issue 2, 2012, Pages 379-389

  Joosse, Simon A ^a   Brandwijk, Kim I M ^a   Devilee, Peter ^b   Wesseling, Jelle ^a   Hogervorst, Frans B L ^a   Verhoef, Senno ^a   Nederlof, Petra M ^a  

^a NETHERLANDS CANCER INSTITUTE   (Netherlands)

^b LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

Array CGH; BRCA1; BRCA2; Breast Cancer; Classifier

Indexed keywords

BRCA1 PROTEIN; BRCA2 PROTEIN; EPIDERMAL GROWTH FACTOR RECEPTOR 2; ESTROGEN RECEPTOR; MESSENGER RNA; PROGESTERONE RECEPTOR; PROTEIN P53;

ADULT; AGED; ARTICLE; BRCA2 GENE; BREAST CARCINOGENESIS; BREAST CARCINOMA; CANCER CLASSIFICATION; CANCER FAMILY; CANCER GRADING; CANCER TISSUE; CHROMOSOME 13Q; CHROMOSOME 14Q; CHROMOSOME 17Q; CHROMOSOME ABERRATION; CLASSIFIER; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; FEMALE; GENE; GENE MUTATION; GENETIC ASSOCIATION; HETEROZYGOSITY LOSS; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; MAJOR CLINICAL STUDY; MEDICAL DECISION MAKING; MICROARRAY ANALYSIS; MUTATIONAL ANALYSIS; NUCLEOTIDE SEQUENCE; OVARY CANCER; PREDICTION; PRIORITY JOURNAL; PROTEIN DEFICIENCY; SENSITIVITY AND SPECIFICITY; VALIDATION PROCESS;

ADULT; AGED; AGED, 80 AND OVER; BRCA1 PROTEIN; BRCA2 PROTEIN; BREAST NEOPLASMS; CARCINOMA, DUCTAL, BREAST; CHROMOSOME ABERRATIONS; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; DNA METHYLATION; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; HEREDITY; HUMANS; IMMUNOHISTOCHEMISTRY; LOSS OF HETEROZYGOSITY; MIDDLE AGED; MUTATION; NEOPLASM INVASIVENESS; NETHERLANDS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHENOTYPE; PREDICTIVE VALUE OF TESTS; PROMOTER REGIONS, GENETIC; RECEPTORS, ESTROGEN; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; TUMOR MARKERS, BIOLOGICAL;

EID: 84859100080     PISSN: 01676806     EISSN: 15737217     Source Type: Journal    
DOI: 10.1007/s10549-010-1016-7     Document Type: Article

References (44)

1. Foulkes WD (2006) BRCA1 and BRCA2: chemosensitivity, treatment outcomes and prognosis. Fam Cancer 5:135-142
2. Rubinstein WS (2008) Hereditary breast cancer: pathobiology, clinical translation, and potential for targeted cancer therapeutics. Fam Cancer 7:83-89
3. Antoniou AC, Hardy R, Walker L, Evans DG, Shenton A, Eeles R, Shanley S, Pichert G, Izatt L, Rose S, Douglas F, Eccles D, Morrison PJ, Scott J, Zimmern RL, Easton DF, Pharoah PD (2008) Predicting the likelihood of carrying a BRCA1 or BRCA2 mutation: validation of BOADICEA, BRCAPRO, IBIS, Myriad and the Manchester scoring system using data from UK genetics clinics. J Med Genet 45:425-431 (Pubitemid 351977132)
4. Hogervorst FB, Cornelis RS, Bout M, van Vliet M, Oosterwijk JC, Olmer R, Bakker B, Klijn JG, Vasen HF, Meijers-Heijboer H (1995) Rapid detection of BRCA1 mutations by the protein truncation test. Nat Genet 10:208-212
5. van der Hout AH, van den Ouweland AM, van der Luijt RB, Gille HJ, Bodmer D, Bruggenwirth H, Mulder IM, van der Vlies P, Elfferich P, Huisman MT, ten Berge AM, Kromosoeto J, Jansen RP, van Zon PH, Vriesman T, Arts N, Lange MB, Oosterwijk JC, Meijers-Heijboer H, Ausems MG, Hoogerbrugge N, Verhoef S, Halley DJ, Vos YJ, Hogervorst F, Ligtenberg M, Hofstra RM (2006) A DGGE system for comprehensive mutation screening of BRCA1 and BRCA2: application in a Dutch cancer clinic setting. Hum Mutat 27:654-666
6. Kang HH, Williams R, Leary J, Ringland C, Kirk J, Ward R (2006) Evaluation of models to predict BRCA germline mutations. Br J Cancer 95:914-920 (Pubitemid 44498108)
7. Carvalho MA, Couch FJ, Monteiro AN (2007) Functional assays for BRCA1 and BRCA2. Int J Biochem Cell Biol 39:298-310 (Pubitemid 44855653)
8. 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 (2005) Distinct genomic profiles in hereditary breast tumors identified by array-based comparative genomic hybridization. Cancer Res 65:7612-7621 (Pubitemid 41297233)
9. Joosse SA, van Beers EH, Tielen IH, Horlings H, Peterse JL, Hoogerbrugge N, Ligtenberg MJ, Wessels LF, Axwijk P, Verhoef S, Hogervorst FB, Nederlof PM (2009) Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH. Breast Cancer Res Treat 116:479-489
10. Tirkkonen M, Johannsson O, Agnarsson BA, Olsson H, Ingvarsson S, Karhu R, Tanner M, Isola J, Barkardottir RB, Borg A, Kallioniemi OP (1997) Distinct somatic genetic changes associated with tumor progression in carriers of BRCA1 and BRCA2 germ-line mutations. Cancer Res 57:1222-1227 (Pubitemid 27152540)
11. van Beers EH, van Welsem T, Wessels LF, Li Y, Oldenburg RA, Devilee P, Cornelisse CJ, Verhoef S, Hogervorst FB, van't Veer Nederlof PM LJ, Nederlof PM (2005) Comparative genomic hybridization profiles in human BRCA1 and BRCA2 breast tumors highlight differential sets of genomic aberrations. Cancer Res 65:822-827 (Pubitemid 40216440)
12. Wessels LF, van Welsem T, Hart AA, van't Veer LJ, Reinders MJ, Nederlof PM (2002) Molecular classification of breast carcinomas by comparative genomic hybridization: a specific somatic genetic profile for BRCA1 tumors. Cancer Res 62:7110-7117 (Pubitemid 35424107)
13. Hedenfalk I, Duggan D, Chen Y, Radmacher M, Bittner M, Simon R, Meltzer P, Gusterson B, Esteller M, Kallioniemi OP, Wilfond B, Borg A, Trent J, Raffeld M, Yakhini Z, Ben Dor A, Dougherty E, Kononen J, Bubendorf L, Fehrle W, Pittaluga S, Gruvberger S, Loman N, Johannsson O, Olsson H, Sauter G (2001) Gene-expression profiles in hereditary breast cancer. N Engl J Med 344:539-548 (Pubitemid 32167867)
14. Van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415:530-536 (Pubitemid 34130608)
15. van den Ouweland AM, Dinjens WN, Dorssers LC, van Veghel-Plandsoen MM, Bruggenwirth HT, Withagen-Hermans CJ, Collee JM, Joosse SA, Terlouw-Kromosoeto JN, Nederlof PM (2009) Deletion ofexons 1a-2 of BRCA1: a rather frequent pathogenic abnormality. Genet Test Mol Biomark 13:399-406
16. Tischkowitz M, Hamel N, Carvalho MA, Birrane G, Soni A, van Beers EH, Joosse SA, Wong N, Novak D, Quenneville LA, Grist SA, Nederlof PM, Goldgar DE, Tavtigian SV, Monteiro AN, Ladias JA, Foulkes WD (2008) Pathogenicity of the BRCA1 missense variant M1775K is determined by the disruption of the BRCT phosphopeptide-binding pocket: a multi-modal approach. Eur J Hum Genet 16:820-832 (Pubitemid 351865680)
17. Lakhani SR, van de Vijver MJ, Jacquemier J, Anderson TJ, Osin PP, McGuffog L, Easton DF (2002) The pathology of familial breast cancer: predictive value of immunohistochemical markers estrogen receptor, progesterone receptor, HER-2, and p53 in patients with mutations in BRCA1 and BRCA2. J Clin Oncol 20:2310-2318 (Pubitemid 34441658)
18. Melchor L, Honrado E, Garcia MJ, Alvarez S, Palacios J, Osorio A, Nathanson KL, Benitez J (2008) Distinct genomic aberration patterns are found in familial breast cancer associated with different immunohistochemical subtypes. Oncogene 27:3165-3175 (Pubitemid 351693170)
19. Stefansson AO, Gunnlaugur JJ, Thor JO, Olafsdottir K, Steinarsdottir M, Valgeirsdottir S, Erla EJ (2009) Genomic profiling of breast tumours in relation to BRCA abnormalities and phenotypes. Breast Cancer Res 11:R47
20. Bergamaschi A, Kim YH, Wang P, Sorlie T, Hernandez-Boussard T, Lonning PE, Tibshirani R, Borresen-Dale AL, Pollack JR (2006) Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer 45:1033-1040 (Pubitemid 44435537)
21. 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 (2006) Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer 6:96
22. Gruvberger S, Ringner M, Chen Y, Panavally S, Saal LH, Borg A, Ferno M, Peterson C, Meltzer PS (2001) Estrogen receptor status in breast cancer is associated with remarkably distinct gene expression patterns. Cancer Res 61:5979-5984 (Pubitemid 32762524)
23. Loo LW, Grove DI, Williams EM, Neal CL, Cousens LA, Schubert EL, Holcomb IN, Massa HF, Glogovac J, Li CI, Malone KE, Daling JR, Delrow JJ, Trask BJ, Hsu L, Porter PL (2004) Array comparative genomic hybridization analysis of genomic alterations in breast cancer subtypes. Cancer Res 64:8541-8549 (Pubitemid 39552066)
24. 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 (2007) Estrogen receptor status could modulate the genomic pattern in familial and sporadic breast cancer. Clin Cancer Res 13:7305-7313
25. HBOC Criteria (2009) Available from http://www.bccancer.bc.ca/HPI/ CancerManagementGuidelines/HereditaryCancerProgram/referralinformation/ hboccriteria.htm (article online)
26. van Beers EH, Joosse SA, Ligtenberg MJ, Fles R, Hogervorst FB, Verhoef S, Nederlof PM (2006) A multiplex PCR predictor for aCGH success of FFPE samples. Br J Cancer 94:333-337 (Pubitemid 43151556)
27. Viale G, Regan MM, Maiorano E, Mastropasqua MG, Dell'Orto P, Rasmussen BB, Raffoul J, Neven P, Orosz Z, Braye S, Ohlschlegel C, Thurlimann B, Gelber RD, Castiglione-Gertsch M, Price KN, Goldhirsch A, Gusterson BA, Coates AS (2007) Prognostic and predictive value of centrally reviewed expression of estrogen and progesterone receptors in a randomized trial comparing letrozole and tamoxifen adjuvant therapy for postmenopausal early breast cancer: BIG 1-98. J Clin Oncol 25:3846-3852 (Pubitemid 47477259)
28. Wolff AC, Hammond ME, Schwartz JN, Hagerty KL, Allred DC, Cote RJ, Dowsett M, Fitzgibbons PL, Hanna WM, Langer A, McShane LM, Paik S, Pegram MD, Perez EA, Press MF, Rhodes A, Sturgeon C, Taube SE, Tubbs R, Vance GH, van de Vijver M, Wheeler TM, Hayes DF (2007) American Society of Clinical Oncology/College of American Pathologists guideline recommendations for human epidermal growth factor receptor 2 testing in breast cancer. J Clin Oncol 25:118-145 (Pubitemid 350003059)
29. oncoline (2008) Available from http://www.oncoline.nl/ (article online)
30. Genestie C, Zafrani B, Asselain B, Fourquet A, Rozan S, Validire P, Vincent-Salomon A, Sastre-Garau X (1998) Comparison of the prognostic value of Scarff-Bloom-Richardson and Nottingham histological grades in a series of 825 cases of breast cancer: major importance of the mitotic count as a component of both grading systems. Anticancer Res 18:571-576 (Pubitemid 28174874)
31. Joosse SA, van Beers EH, Nederlof PM (2007) Automated array-CGH optimized for archival formalin-fixed, paraffin-embedded tumor material. BMC Cancer 7:43
32. Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207-210 (Pubitemid 34679544)
33. Picard F, Robin S, Lavielle M, Vaisse C, Daudin JJ (2005) A statistical approach for array CGH data analysis. BMC Bioinformatics 6:27
34. Chin SF, Teschendorff AE, Marioni JC, Wang Y, Barbosa-Morais NL, Thorne NP, Costa JL, Pinder SE, van de Wiel MA, Green AR, Ellis IO, Porter PL, Tavare S, Brenton JD, Ylstra B, Caldas C (2007) High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. Genome Biol 8:R215
35. Joosse SA (2010) Fisher's exact test. Available from http://in-silico. net/Statistics/Fisher-exact-test (article online)
36. Dobbin KK, Zhao Y, Simon RM (2008) How large atraining set is needed to develop a classifier for microarray data? Clin Cancer Res 14:108-114 (Pubitemid 351377984)
37. Tibshirani R, Hastie T, Narasimhan B, Chu G (2002) Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci USA 99:6567-6572 (Pubitemid 34526173)
38. Kontorovich T, Cohen Y, Nir U, Friedman E (2008) Promoter methylation patterns of ATM, ATR, BRCA1, BRCA2 and P53 as putative cancer risk modifiers in Jewish BRCA1/BRCA2 mutation carriers. Breast Cancer Res Treat 116:195-200
39. Dworkin AM, Spearman AD, Tseng SY, Sweet K, Toland AE (2009) Methylation not afrequent "second hit" in tumors with germline BRCA mutations. Fam Cancer 8:339-346
40. Xia F, Taghian DG, DeFrank JS, Zeng ZC, Willers H, Iliakis G, Powell SN (2001) Deficiency of human BRCA2 leads to impaired homologous recombination but maintains normal nonhomologous end joining. Proc Natl Acad Sci USA 98:8644-8649 (Pubitemid 32678081)
41. Moynahan ME, Chiu JW, Koller BH, Jasin M (1999) Brca1 controls homology-directed DNA repair. Mol Cell 4:511-518 (Pubitemid 29531131)
42. Scully R, Ganesan S, Vlasakova K, Chen J, Socolovsky M, Livingston DM (1999) Genetic analysis of BRCA1 function in a defined tumor cell line. Mol Cell 4:1093-1099 (Pubitemid 30054915)
43. Durant ST, Nickoloff JA (2005) Good timing in the cell cycle for precise DNA repair by BRCA1. Cell Cycle 4:1216-1222 (Pubitemid 41365391)
44. Vollebergh MA, Nederlof PM, Wessels LF, Schmidt MK, Joosse SA, van Beers E, Froklage F, Holtkamp M, Schrama JG, Wesseling J, Hauptmann M, de Bruin M, Rodenhuis S, Linn SC (2009) Predicting response toalkylating chemotherapy in breast cancer patients using array comparative genomic hybridization. Cancer Res 69:361S-362S