Genome-wide genetic characterization of bladder cancer: A comparison of high-density single-nucleotide polymorphism arrays and PCR-based microsatellite analysis

Cancer Research

Volumn 63, Issue 9, 2003, Pages 2216-2222

  Hoque, Mohammad Obaidul ^a   Lee, Chyi Chia R ^a   Cairns, Paul ^b   Schoenberg, Mark ^c   Sidransky, David ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b FOX CHASE CANCER CENTER   (United States)

^c DEPARTMENT OF PATHOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALLELE; ALLELIC IMBALANCE; ALLOTYPE; ANALYTIC METHOD; ARTICLE; BLADDER; BLADDER CANCER; CANCER GENETICS; CHROMOSOMAL PARAMETERS; CHROMOSOME 12Q; CHROMOSOME 16P; CHROMOSOME 1P; CHROMOSOME 2Q; CHROMOSOME ARM; CLINICAL ARTICLE; CONTROLLED STUDY; DNA MICROARRAY; GENE LOCUS; GENE MAPPING; GENETIC ANALYSIS; GENOMICS; GENOTYPE; HETEROZYGOSITY LOSS; HUMAN; HUMAN CELL; HUMAN TISSUE; INTERMETHOD COMPARISON; MICROSATELLITE MARKER; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SAMPLE; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSITIONAL CELL CARCINOMA; TUMOR; TUMOR RECURRENCE; VALIDATION PROCESS;

CARCINOMA, TRANSITIONAL CELL; CHROMOSOME ABERRATIONS; GENOME, HUMAN; HUMANS; LOSS OF HETEROZYGOSITY; MICROSATELLITE REPEATS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; URINARY BLADDER NEOPLASMS;

EID: 0037699066     PISSN: 00085472     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (35)

1. Fearon, E. R., and Vogelstein, B. A genetic model for colorectal tumorigenesis. Cell, 61: 759-767, 1990.
2. Knudson, A. G., Jr. Hereditary cancer, oncogenes, and antioncogenes. Cancer Res., 45: 1437-1443, 1985.
3. Vogelstein, B., Fearon, E. R., Kern, S. E., Hamilton, S. R., Preisinger, A. C., Nakamura, Y., and White, R. Allelotype of colorectal carcinomas. Science (Wash. DC), 244: 207-211, 1989.
4. Weissenbach, J., Gyapay, G., Dib, C., Vignal, A., Morissette, J., Millasseau, P., Vaysseix, G., and Lathrop, M. A second-generation linkage map of the human genome. Nature (Lond.), 359: 794-801, 1992.
5. Pollack, J. R., Perou, C. M., Alizadeh, A. A., Eisen, M. B., Pergamenschikov, A., Williams, C. F., Jeffrey, S. S., Botstein, D., and Brown, P. O. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat. Genet., 23: 41-46, 1999.
6. Mei, R., Galipeau, P. C., Prass, C., Berno, A., Ghandour, G., Patil, N., Wolff, R. K., Chee, M. S., Reid, B. J., and Lockhart, D. J. Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res., 10: 1126-1137, 2000.
7. Lindblad-Toh, K., Tanenbaum, D. M., Daly, M. J., Winchester, E., Lui, W. O., Villapakkam, A., Stanton, S. E., Larsson, C., Hudson, T. J., Johnson, B. E., Lander, E. S., and Meyerson, M. Loss-of-heterozygosity analysis of small-cell lung carcinomas using single-nucleotide polymorphism arrays. Nat. Biotechnol., 18: 1001-1005, 2000.
8. Forozan, F., Karhu, R., Kononen, J., Kallioniemi, A., and Kallioniemi, O. P. Genome screening by comparative genomic hybridization. Trends Genet., 13: 405-409, 1997.
9. Kruglyak, L. The use of a genetic map of biallelic markers in linkage studies. Nat. Genet., 17: 21-24, 1997.
10. Gibas, Z., and Gibas, L. Cytogenetics of bladder cancer. Cancer Genet. Cytogenet., 95: 108-115, 1997.
11. Nawroz, H., Koch, W., Anker, P., Stroun, M., and Sidransky, D. Microsatellite alterations in serum DNA of head and neck cancer patients. Nat Med., 2: 1035-1037, 1996.
12. SAS Institute Inc. SAS User's Guide: Statistics, Version 5 Ed. Cary, NC: SAS Institute Inc., 1985.
13. Richter, J., Beffa, L., Wagner, U., Schraml, P., Gasser, T. C., Moch, H., Mihatsch, M. J., and Sauter, G. Patterns of chromosomal imbalances in advanced urinary bladder cancer detected by comparative genomic hybridization. Am. J. Pathol., 153: 1615-1621, 1998.
14. Tsai, Y. C., Nichols, P. W., Hiti, A. L., Williams, Z., Skinner, D. G., and Jones, P. A. Allelic losses of chromosomes 9, 11, and 17 in human bladder cancer. Cancer Res., 50: 44-47, 1990.
15. Reznikoff, C. A., Belair, C. D., Yeager, T. R., Savelieva, E., Blelloch, R. H., Puthenveettil, J. A., and Cuthill, S. A molecular genetic model of human bladder cancer pathogenesis. Semin. Oncol., 23: 571-584, 1996.
16. Cairns, P., Mao, L., Merlo, A., Lee, D. J., Schwab, D., Eby, Y., Tokino, K., van der Riet, P., Blaugrund, J. E., and Sidransky, D. Rates of p16 (MTS1) mutations in primary tumors with 9p loss. Science (Wash. DC), 265: 415-417, 1994.
17. Gruis, N. A., Abeln, E. C., Bardoel, A. F., Devilee, P., Frants, R. R., and Cornelisse, C. J. PCR-based microsatellite polymorphisms in the detection of loss of heterozygosity in fresh and archival tumour tissue. Br. J. Cancer, 68: 308-313, 1993.
18. Cairns, P., Polascik, T. J., Eby, Y., Tokino, K., Califano, J., Merlo, A., Mao, L., Herath, J., Jenkins, R., Westra, W., et al. Frequency of homozygous deletion at p16/CDKN2 in primary human tumours. Nat. Genet., 11: 210-212, 1995.
19. Chang, W. Y., Cairns, P., Schoenberg, M. P., Polascik, T. J., and Sidransky, D. Novel suppressor loci on chromosome 14q in primary bladder cancer. Cancer Res., 55: 3246-3249, 1995.
20. Mahdy, E., Yoshihiro, S., Zech, L., Wester, K., Pan, Y., Busch, C., Dohner, H., Kallioniemi, O., Bergerheim, U., and Malmstrom, P. U. Comparison of comparative genomic hybridization, fluorescence in situ hybridization and flow cytometry in urinary bladder cancer. Anticancer Res., 19: 7-12, 1999.
21. Hartmann, A., Rosner, U., Schlake, G., Dietmaier, W., Zaak, D., Hofstaedter, F., and Knuechel, R. Clonality and genetic divergence in multifocal low-grade superficial urothelial carcinoma as determined by chromosome 9 and p53 deletion analysis. Lab. Investig., 80: 709-718, 2000.
22. Hartmann, A., Schlake, G., Zaak, D., Hungerhuber, E., Hofstetter, A., Hofstaedter, F., and Knuechel, R. Occurrence of chromosome 9 and p53 alterations in multifocal dysplasia and carcinoma in situ of human urinary bladder. Cancer Res., 62: 809-818, 2002.
23. Cairns, J. P., Ching, P. W., Ramamoorthy, S., Kurnit, D. M., and Sidransky D. A comparison between microsatellite and quantitative PCR analyses to detect frequent p16 copy number changes in primary bladder tumors. Clin. Cancer Res., 4: 441-444, 1998.
24. Wang, D. G., Fan, J. B., Siao, C. J., Berno, A., Young, P., Sapolsky, R., Ghandour, G., Perkins, N., Winchester, E., Spencer, J., Kruglyak, L., Stein, L., Hsie, L., Topaloglou, T., Hubbell, E., Robinson, E., Mittmann, M., Morris, M. S., Shen, N., Kilbum, D., Rioux, J., Nusbaum, C., Rozen, S., Hudson, T. J., Lander, E. S., et al. Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science (Wash. DC), 280: 1077-1082, 1998.
25. Greer, C. E., Lund, J. K., and Manos, M. M. PCR amplification from paraffin-embedded tissues: recommendations on fixatives for long-term storage and prospective studies. PCR Methods Appl., 1: 46-50, 1991.
26. Ben-Ezra, J., Johnson, D. A., Rossi, J., Cook, N., and Wu, A. Effect of fixation on the amplification of nucleic acids from paraffin-embedded material by the polymerase chain reaction. J. Histochem. Cytochem., 39: 351-354, 1991.
27. Schubert, E. L., Hsu, L., Cousens, L. A., Glogovac, J., Self, S., Reid, B. J., Rabinovitch, P. S., and Porter, P. L. Single nucleotide polymorphism array analysis of flow-sorted epithelial cells from frozen versus fixed tissues for whole genome analysis of allelic loss in breast cancer. Am. J. Pathol., 160: 73-79, 2002.
28. Kallioniemi, A., Kallioniemi, O. P., Citro, G., Sauter, G., DeVries, S., Kerschmann, R., Caroll, P., and Waldman, F. Identification of gains and losses of DNA sequences in primary bladder cancer by comparative genomic hybridization. Genes Chromosomes Cancer, 12: 213-219, 1995.
29. Cairns, P., Shaw, M. E., and Knowles, M. A. Preliminary mapping of the deleted region of chromosome 9 in bladder cancer. Cancer Res., 53: 1230-1232, 1993.
30. Williamson, M. P., Elder, P. A., Shaw, M. E., Devlin, J., and Knowles, M. A. p16 (CDKN2) is a major deletion target at 9p21 in bladder cancer. Hum. Mol. Genet., 4: 1569-1577, 1995.
31. Orlow, I., Lianes, P., Lacombe, L., Dalbagni, G., Reuter, V. E., and Cordon-Cardo, C. Chromosome 9 allelic losses and microsatellite alterations in human bladder tumors. Cancer Res., 54: 2848-2851, 1994.
32. Tanaka, M., Mullauer, L., Ogiso, Y., Fujita, H., Moriya, S., Furuuchi, K., Harabayashi, T., Shinohara, N., Koyanagi, T., and Kuzumaki, N. Gelsolin: a candidate for suppressor of human bladder cancer. Cancer Res., 55: 3228-3232, 1995.
33. Koo, S. H., Kwon, K. C., Ihm, C. H., Jeon, Y. M., Park, J. W., and Sul, C. K. Detection of genetic alterations in bladder tumors by comparative genomic hybridization and cytogenetic analysis. Cancer Genet. Cytogenet., 110: 87-93, 1999.
34. Takle, L. A., and Knowles, M. A. Deletion mapping implicates two tumor suppressor genes on chromosome 8p in the development of bladder cancer. Oncogene, 12: 1083-1087, 1996.
35. Primdahl, H., Wikman, F. P., von der Maase, H., Zhou, X. G., Wolf, H., and Orntoft, T. F. Allelic imbalances in human bladder cancer: genome-wide detection with high-density single-nucleotide polymorphism arrays. J. Natl. Cancer Inst. (Bethesda), 94: 216-223, 2002.