Copy-number analysis of topoisomerase and thymidylate synthase genes in frozen and FFPE DNAs of colorectal cancers

Pharmacogenomics

Volumn 9, Issue 10, 2008, Pages 1459-1466

  Yu, Jinsheng ^a   Miller, Ryan ^a,b   Zhang, Wanghai ^a   Sharma, Mala ^a   Holtschlag, Vicky ^a   Watson, Mark A ^a   McLeod, Howard L ^b  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

Colorectal cancer; DNA copy number; Formalin fixed paraffin embedded tissue; Quantitative PCR; Thymidylate synthase; Topoisomerase I

Indexed keywords

DNA; DNA TOPOISOMERASE; EPIDERMAL GROWTH FACTOR RECEPTOR; FORMALDEHYDE; PARAFFIN; RNA; THYMIDYLATE SYNTHASE;

ADULT; AGED; ARTICLE; CANCER CHEMOTHERAPY; COLORECTAL CANCER; CONTROLLED STUDY; DIPLOIDY; FEMALE; GENE AMPLIFICATION; GENE DELETION; GENOME ANALYSIS; GENOMICS; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; MALE; OUTCOMES RESEARCH; PHARMACOGENETICS; PHARMACOGENOMICS; POLYMERASE CHAIN REACTION; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; RELIABILITY;

ADULT; AGED; AGED, 80 AND OVER; CASE-CONTROL STUDIES; COLORECTAL NEOPLASMS; DNA TOPOISOMERASES, TYPE I; DNA, NEOPLASM; FEMALE; FORMALDEHYDE; FREEZING; GENE DOSAGE; HUMANS; IMMUNOHISTOCHEMISTRY; MALE; MIDDLE AGED; NEOPLASM STAGING; PARAFFIN EMBEDDING; THYMIDYLATE SYNTHASE; TISSUE FIXATION;

EID: 55449094139     PISSN: 14622416     EISSN: 17448042     Source Type: Journal    
DOI: 10.2217/14622416.9.10.1459     Document Type: Article

References (19)

1. Ouahchi K, Lindeman N, Lee C: Copy number variants and pharmacogenomics. Pharmacogenomics 7, 25-29 (2006).
2. Cheng Q, Yang W, Raimondi SC, Pui CH, Relling MV, Evans WE: Karyotypic abnormalities create discordance of germline genotype and cancer cell phenotypes. Nat. Genet. 37, 878-882 (2005).
3. Brody JR, Hucl T, Gallmeier E, Winter JM, Kern SE, Murphy KM: Genomic copy number changes affecting the thymidylate synthase (TYMS) gene in cancer: a model for patient classification to aid fluoropyrimidine therapy. Cancer Res. 66, 9369-9373 (2006).
4. Wang TL, Diaz LA Jr, Romans K et al.: Digital karyotyping identifies thymidylate synthase amplification as a mechanism of resistance to 5-fluorouracil in metastatic colorectal cancer patients. Proc. Natl Acad. Sci. USA 101, 3089-3094 (2004).
5. Moroni M, Veronese S, Benvenuti S et al.: Gene copy number for epidermal growth factor receptor (EGFR) and clinical response to anti-EGFR treatment in colorectal cancer: a cohort study. Lancet Oncol. 6, 279-286 (2005).
6. Devries S, Nyante S, Korkola J et al.: Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors. J. Mol. Diagn. 7, 65-71 (2005).
7. Jacobs S, Thompson ER, Nannya Y et al.: Genome-wide, high-resolution detection of copy number, loss of heterozygosity, and genotypes from formalin-fixed, paraffin-embedded tumor tissue using microarrays. Cancer Res. 67, 2544-2551 (2007).
8. Antonov J, Goldstein DR, Oberli A et al.: Reliable gene expression measurements from degraded RNA by quantitative real-time PCR depend on short amplicators and a proper normalization. Lab. Invest. 85, 1040-1050 (2005).
9. Lehmann U, Kreipe H: Real-time PCR analysis of DNA and RNA extracted from formalin-fixed and paraffin-embedded biopsies. Methods 25, 409-418 (2001).
10. Godfrey TE, Kim SH, Chavira M et al.: Quantitative mRNA expression analysis from formalin-fixed, paraffin-embedded tissues using 5′ nuclease quantitative reverse transcription-polymerase chain reaction. J. Mol. Diagn. 2, 84-91 (2000).
11. Rooney PH, Boonsong A, McKay JA et al.: Colorectal cancer genomics: evidence for multiple genotypes which influence survival. Br. J. Cancer 85, 1492-1498 (2001).
12. Kidd EA, Yu J, Li X, Shannon WD, Watson MA, McLeod HL: Variance in the expression of 5-fluorouracil pathway genes in colorectal cancer. Clin. Cancer Res. 11, 2612-2619 (2005).
13. Yu J, Shannon WD, Watson MA, McLeod HL: Gene expression profiling of the irinotecan pathway in colorectal cancer. Clin. Cancer Res. 11, 2053-2062 (2005).
14. Zhang W, Shannon WD, Duncan J, Scheffer GL, Scheper RJ, McLeod HL: Expression of drug pathway proteins is independent of tumour type. J. Pathol. 209, 213-219 (2006).
15. Konigshoff M, Wilhelm J, Bohle RM, Pingoud A, Hahn M: HER-2/neu gene copy number quantified by real-time PCR: comparison of gene amplification, heterozygosity, and immunohistochemical status in breast cancer tissue. Clin. Chem. 49, 219-229 (2003).
16. Weksberg R, Hughes S, Moldovan L, Bassett AS, Chow EW, Squire JA: A method for accurate detection of genomic microdeletions using real-time quantitative PCR. BMC Genomics 6, 180 (2005).
17. Miller CR, Dunham CP, Scheithauer BW, Perry A: Significance of necrosis in grading of oligodendroglial neoplasms: a clinicopathologic and genetic study of newly diagnosed high-grade gliomas. J. Clin. Oncol. 24, 5419-5426 (2006).
18. Halling KC, Kipp BR: Fluorescence in situ hybridization in diagnostic cytology. Hum. Pathol. 38, 1137-1144 (2007).
19. Rooney PH, Boonsong A, McFadyen MC et al.: The candidate oncogene ZNF217 is frequently amplified in colon cancer. J. Pathol. 204, 282-288 (2004).