Somatic sequence alterations in twenty-one genes selected by expression profile analysis of breast carcinomas

Breast Cancer Research

Volumn 9, Issue 1, 2007, Pages

  Chanock, Stephen J ^a   Burdett, Laurie ^a,b   Yeager, Meredith ^a,b   Llaca, Victor ^b   Langerød, Anita ^c   Presswalla, Shafaq ^a,b   Kaaresen, Rolf ^c   Strausberg, Robert L ^d   Gerhard, Daniela S ^a   Kristensen, Vessela ^a,c,e   Perou, Charles M ^f   Børresen Dale, Anne Lise ^c,e  

^a NATIONAL CANCER INSTITUTE   (United States)

^b SAIC FREDERICK INC   (United States)

^c OSLO UNIVERSITY HOSPITAL   (Norway)

^d J CRAIG VENTER INSTITUTE   (United States)

^e UNIVERSITY OF OSLO   (Norway)

^f UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREAST CARCINOMA; CANCER STAGING; GENE DELETION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENE INSERTION; GENE MUTATION; GENE SEQUENCE; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; MISSENSE MUTATION; MUTATIONAL ANALYSIS; NUCLEIC ACID BASE SUBSTITUTION; PROGNOSIS; SEQUENCE ANALYSIS; TUMOR GENE; TUMOR SUPPRESSOR GENE; BREAST TUMOR; CARCINOMA; EXON; FEMALE; GENETICS; NUCLEOTIDE SEQUENCE;

BREAST NEOPLASMS; CARCINOMA; CONSERVED SEQUENCE; DNA MUTATIONAL ANALYSIS; EXONS; FEMALE; GENE EXPRESSION PROFILING; HUMANS;

EID: 33847298866     PISSN: 14655411     EISSN: 1465542X     Source Type: Journal    
DOI: 10.1186/bcr1637     Document Type: Article

References (44)

1. Balmain A Gray J Ponder B The genetics and genomics of cancer Nat Genet 2003, 33:238-244 12610533
2. Wang TL Rago C Silliman N Ptak J Markowitz S Willson JK Parmigiani G Kinzler KW Vogelstein B Velculescu VE Prevalence of somatic alterations in the colorectal cancer cell genome Proc Natl Acad Sci USA 2002, 99:3076-3080 122475 11867767
3. Weir B Zhao X Meyerson M Somatic alterations in the human cancer genome Cancer Cell 2004, 6:433-438 15542426
4. Langerod A Bukholm IR Bregard A Lonning PE Andersen TI Rognum TO Meling GI Lothe RA Borresen-Dale AL The TP53 codon 72 polymorphism may affect the function of TP53 mutations in breast carcinomas but not in colorectal carcinomas Cancer Epidemiol Biomarkers Prev 2002, 11:1684-1688 12496062
5. Børresen-Dale A-L TP53 and breast cancer Hum Mutat 2003, 21:292-300 12619115
6. Olivier M Langerød A Carrieri P Bergh J Klaar S Eyfjord J Theillet C Rodriguez C Lidereau R Bieche I The clinical value of somatic TP53 gene mutations in 1,794 patients with breast cancer Clin Cancer Res 2006, 12:1157-1167 16489069
7. Samuels Y Wang Z Bardelli A Silliman N Ptak J Szabo S Yan H Gazdar A Powell SM Riggins GJ High frequency of mutations of the PIK3CA gene in human cancers Science 2004, 304:554 15016963
8. Wu G Xing M Mambo E Huang X Liu J Guo Z Chatterjee A Goldenberg D Gollin SM Sukumar S Somatic mutation and gain of copy number of PIK3CA in human breast cancer Breast Cancer Res 2005, 7:R609-R616 1242128 16168105
9. Kurose K Gilley K Matsumoto S Watson PH Zhou XP Eng C Frequent somatic mutations in PTEN and TP53 are mutually exclusive in the stroma of breast carcinomas Nat Genet 2002, 32:355-357 12379854
10. Bachman KE Argani P Samuels Y Silliman N Ptak J Szabo S Konishi H Karakas B Blair BG Lin C The PIK3CA gene is mutated with high frequency in human breast cancers Cancer Biol Ther 2004, 3:772-775 15254419
11. Campbell IG Russell SE Choong DY Montgomery KG Ciavarella ML Hooi CS Cristiano BE Pearson RB Phillips WA Mutation of the PIK3CA gene in ovarian and breast cancer Cancer Res 2004, 64:7678-7681 15520168
12. Wang Z Shen D Parsons DW Bardelli A Sager J Szabo S Ptak J Silliman N Peters BA van der Heijden MS Mutational analysis of the tyrosine phosphatome in colorectal cancers Science 2004, 304:1164-1166 15155950
13. Davies H Bignell GR Cox C Stephens P Edkins S Clegg S Teague J Woffendin H Garnett MJ Bottomley W Mutations of the BRAF gene in human cancer Nature 2002, 417:949-954 12068308
14. Parsons DW Wang TL Samuels Y Bardelli A Cummins JM DeLong L Silliman N Ptak J Szabo S Willson JK Colorectal cancer: Mutations in a signalling pathway Nature 2005, 436:792 16094359
15. Stephens P Edkins S Davies H Greenman C Cox C Hunter C Bignell G Teague J Smith R Stevens C A screen of the complete protein kinase gene family identifies diverse patterns of somatic mutations in human breast cancer Nat Genet 2005, 37:590-592 15908952
16. Sjoblom T Jones S Wood LD Parsons DW Lin J Barber T Mandelker D Leary RJ Ptak J Silliman N The consensus coding sequences of human breast and colorectal cancers Science 2006, 314:268-274 16959974
17. Perou CM Sorlie T Eisen MB van de Rijn M Jeffrey SS Rees CA Pollack JR Ross DT Johnsen H Akslen LA Molecular portraits of human breast tumours Nature 2000, 406:747-752 10963602
18. Sorlie T Perou CM Tibshirani R Aas T Geisler S Johnsen H Hastie T Eisen MB van den Rijn M Jeffrey SS Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications Proc Natl Acad Sci USA 2001 98 10869 10874 58566 11553815
19. Sorlie T Tibshirani R Parker J Hastie T Marron JS Nobel A Deng S Johnsen H Pesich R Geisler S Repeated observation of breast tumor subtypes in independent gene expression data sets Proc Natl Acad Sci USA 2003, 100:8418-8423 166244 12829800
20. 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
21. Rozen S Skaletsky HJ Bioinformatics Methods and Protocols: Methods in Molecular Biology Totowa, NJ: Humana Press 2000, 365-386
22. Packer BR Yeager M Burdett L Welch R Beerman M Qi L Sicotte H Staats B Acharya M Crenshaw A SNP500Cancer: A public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes Nucleic Acids Res 2006, 34:D617-D621 1347513 16381944
23. Mayor C Brudno M Schwartz JR Poliakov A Rubin EM Frazer KA Pachter LS Dubchak I VISTA: Visualizing global DNA sequence alignments of arbitrary length Bioinformatics 2000, 16: 1046-1047 11159318
24. Helle SI Ekse D Holly JMP Lonning PE The IGF-system in healthy pre- and postmenopausal women: Relations to demographic variables and sex-steroids J Steroid Biochem Mol Biol 2002, 81:95-102 12127047
25. Benito M Parker J Du Q Wu J Xiang D Perou CM Marron JS Adjustment of systematic microarray data biases Bioinformatics 2004, 20:105-114 14693816
26. Diehn M Sherlock G Binkley G Jin H Matese JC Hernandez-Boussard T Rees CA Cherry JM Botstein D Brown PO SOURCE: A unified genomic resource of functional annotations, ontologies, and gene expression data Nucleic Acids Res 2003, 31:219-223 165461 12519986
27. Yang YH Dudoit S Luu P Lin DM Peng V Ngai J Speed TP Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res 2002, 30:e15 100354 11842121
28. Troyanskaya O Cantor M Sherlock G Brown P Hastie T Tibshirani R Botstein D Altman RB Missing value estimation methods for DNA microarrays Bioinformatics 2001, 17:520-525 11395428
29. Usary J Llaca V Karaca G Presswala S Karaca M He X Langerod A Karesen R Oh DS Dressler LG Mutation of GATA3 in human breast tumors Oncogene 2004, 23:7669-7678 15361840
30. Miyata T Miyazawa S Yasunaga T Two types of amino acid substitutions in protein evolution J Mol Evol 1979, 12:219-236 439147
31. Rieger-Christ KM Pezza JA Dugan JM Braasch JW Hughes KS Summerhayes IC Disparate E-cadherin mutations in LCIS and associated invasive breast carcinomas Mol Pathol 2001, 54:91-97 1187009 11322170
32. Berx G Becker KF Hofler H van Roy F Mutations of the human E-cadherin (CDH1) gene Hum Mutat 1998, 12:226-237 9744472
33. Graff JR Herman JG Lapidus RG Chopra H Xu R Jarrard DF Isaacs WB Pitha PM Davidson NE Baylin SB E-cadherin expression is silenced by DNA hypermethylation in human breast and prostate carcinomas Cancer Res 1995, 55:5195-5199 7585573
34. Berx G Cleton-Jansen AM Strumane K de Leeuw WJ Nollet F van Roy F Cornelisse C E-cadherin is inactivated in a majority of invasive human lobular breast cancers by truncation mutations throughout its extracellular domain Oncogene 1996, 13:1919-1925 8934538
35. The International HapMap Consortium The International HapMap Project Nature 2005, 437:1299-1320 16255080
36. Gerhard DS Wagner L Feingold EA Shenmen CM Grouse LH Schuler G Klein SL Old S Rasooly R Good P The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC) Genome Res 2004, 14:2121-2127 528928 15489334
37. Chano T Kontani K Teramoto K Okabe H Ikegawa S Truncating mutations of RB1CC1 in human breast cancer Nat Genet 2002, 31:285-288 12068296
38. Wulf G Ryo A Liou YC Lu KP The prolyl isomerase Pin1 in breast development and cancer Breast Cancer Res 2003, 5:76-82 154150 12631385
39. Ekholm-Reed S Spruck CH Sangfelt O van Drogen F Mueller-Holzner E Widschwendter M Zetterberg A Reed SI Mutation of hCDC4 leads to cell cycle deregulation of cyclin E in cancer Cancer Res 2004, 64:795-800 14871801
40. Strohmaier H Spruck CH Kaiser P Won KA Sangfelt O Reed SI Human F-box protein hCdc4 targets cyclin E for proteolysis and is mutated in a breast cancer cell line Nature 2001, 413:316-322 11565034
41. Sørlie T Vu P Johnsen H Lind GE Lothe RA Børresen-Dale A-L Mutation screening of the TP53 gene by temporal temperature gel electrophoresis (TTGE) Methods in Molecular Biology. Molecular Toxicology Protocols Totowa, NJ: Humana Press Inc Keohavong P, Grant SG 2004, 291:207-216
42. Geisler S Borresen-Dale AL Johnsen H Aas T Geisler J Akslen LA Anker G Lonning PE TP53 gene mutations predict the response to neoadjuvant treatment with 5-fluorouracil and mitomycin in locally advanced breast cancer Clin Cancer Res 2003, 9:5582-5588 14654539
43. Lynch TJ Bell DW Sordella R Gurubhagavatula S Okimoto RA Brannigan BW Harris PL Haserlat SM Supko JG Haluska FG Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib N Engl J Med 2004, 350:2129-2139 15118073
44. Paez JG Janne PA Lee JC Tracy S Greulich H Gabriel H Herman P Kaye FJ Lindeman N Boggon TJ EGFR mutations in lung cancer: Correlation with clinical response to gefitinib therapy Science 2004, 304:1497-1500 15118125