Advertisement

Determination of Cancer Allelotype

  • Jennifer J. Ascaño
  • Steven M. Powell
Part of the Methods in Molecular Biology™ book series (MIMB, volume 222)

Abstract

The term “allelotype” was first used by Vogelstein and colleagues (1), in analogy to karyotype, to describe a newly developed molecular analysis that surveyed chromosomal loss and/or aberration in a panel of human colorectal tumors. This study was the first to comprehensively screen 39 nonacrocentric chromosomal arms in surveying restriction fragment polymorphisms (RFLPs) using variable number tandem repeats (VNTRs) as probes. Simple tandem repeats, including VNTRs and microsatellite loci consisting of 1- to 5-bp repeats, have been found to be highly polymorphic and relatively stable among the human population, which facilitates the analysis of both maternal and paternal alleles. These markers have also been useful in linkage analysis when studying hereditary human disease (2, 3, 4, 5).

Keywords

Polymerase Chain Reaction Product Bottom Plate Variable Number Tandem Repeat Acinar Cell Carcinoma Dark Bottle 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Vogelstein, B., Fearon, E. R., Kern, S. E., et al. (1989) Allelotype of colorectal carcinomas. Science 244, 207–211.PubMedCrossRefGoogle Scholar
  2. 2.
    Jeffreys, A. J., Wilson, V., and Thein, S. L. (1985) Hypervariable “minisatellite” regions in human DNA. Nature 314, 67–73.PubMedCrossRefGoogle Scholar
  3. 3.
    Nakamura, Y., Leppert, M., O’Connell, P., et al. (1987) Variable number of tandem repeat (VNTR) markers for human gene mapping. Science 235, 1616–1622.PubMedCrossRefGoogle Scholar
  4. 4.
    Dib, C., Faure, S., Fizames, C., et al. (1996) A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380, 152–154.PubMedCrossRefGoogle Scholar
  5. 5.
    Hearne, C. M., Ghosh, S., and Todd, J. A. (1992) Microsatellites for linkage analysis of genetic traits. Trends Genet. 8, 288–294.PubMedGoogle Scholar
  6. 6.
    Goelz, S. E., Hamilton, S. R., and Vogelstein, B. (1985) Purification of DNA from formaldehyde fixed and paraffin embedded human tissue. Biochem. Biophys. Res. Commun. 130, 118–126.PubMedCrossRefGoogle Scholar
  7. 7.
    Fearon, E. R., Feinberg, A. P., Hamilton, S. H., and Vogelstein, B. (1985) Loss of genes on the short arm of chromosome 11 in bladder cancer. Nature 318, 377–380.PubMedCrossRefGoogle Scholar
  8. 8.
    Weber, J. L. and May, P. E. (1989) Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am. J. Hum. Genet. 44, 388–396.PubMedGoogle Scholar
  9. 9.
    Yustein, A. S., Harper, J. C., Petroni, G. R., Cummings, O. W., Moskaluk, C. A., and Powell, S. M. (1999) Allelotype of gastric adenocarcinoma. Cancer Res. 59, 1437–1441.PubMedGoogle Scholar
  10. 10.
    Rosin, M. P., Cairns, P., Epstein, J. I., Schoenberg, M. P., and Sidransky, D. (1995) Partial allelotype of carcinoma in situ of the human bladder. Cancer Res. 55, 5213–5216.PubMedGoogle Scholar
  11. 11.
    Shibagaki, I., Shimada, Y., Wagata, T., Ikenaga, M., Imamura, M., and Ishizaki, K. (1994) Allelotype analysis of esophageal squamous cell carcinoma. Cancer Res. 54, 2996–3000.PubMedGoogle Scholar
  12. 12.
    Califano, J. A., Johns, M. M., 3rd, Westra, W. H., et al. (1996) An allelotype of papillary thyroid cancer. Int. J. Cancer 69, 442–444.PubMedCrossRefGoogle Scholar
  13. 13.
    Johns, M. M., 3rd, Westra, W. H., Califano, J. A., Eisele, D., Koch, W. M., and Sidransky, D. (1996) Allelotype of salivary gland tumors. Cancer Res. 56, 1151–1154.PubMedGoogle Scholar
  14. 14.
    Tamura, G., Sakata, K., Nishizuka, S., et al. (1996) Allelotype of adenoma and differentiated adenocarcinoma of the stomach. J. Pathol. 180, 371–377.PubMedCrossRefGoogle Scholar
  15. 15.
    Sano, T., Tsujino, T., Yoshida, K., et al. (1991) Frequent loss of heterozygosity on chromosomes 1q, 5q, and 17p in human gastric carcinomas. Cancer Res. 51, 2926–2931.PubMedGoogle Scholar
  16. 16.
    Seymour, A. B., Hruban, R. H., Redston, M., et al. (1994) Allelotype of pancreatic adeno-carcinoma. Cancer Res. 54, 2761–2764.PubMedGoogle Scholar
  17. 17.
    Rigaud, G., Missiaglia, E., Moore, P. S., et al. (2001) High resolution allelotype of nonfunctional pancreatic endocrine tumors: identification of two molecular subgroups with clinical implications. Cancer Res. 61, 285–292.PubMedGoogle Scholar
  18. 18.
    Rigaud, G., Moore, P. S., Zamboni, G., et al. (2000) Allelotype of pancreatic acinar cell carcinoma. Int. J. Cancer 88, 772–777.PubMedCrossRefGoogle Scholar
  19. 19.
    Shao, J. Y., Wang, H. Y., Huang, X. M., et al. (2000) Genome-wide allelotype analysis of sporadic primary nasopharyngeal carcinoma from southern China. Int. J. Oncol. 17, 1267–1275.PubMedGoogle Scholar
  20. 20.
    Lo, K. W., Teo, P. M., Hui, A. B., et al. (2000) High resolution allelotype of microdissected primary nasopharyngeal carcinoma. Cancer Res. 60, 3348–3353.PubMedGoogle Scholar
  21. 21.
    Roncalli, M., Borzio, M., Bianchi, P., and Laghi, L. (2000) Comprehensive allelotype study of hepatocellular carcinoma. Hepatology 32, 876.PubMedCrossRefGoogle Scholar
  22. 22.
    Kang, Y. K., Kim, Y. I., and Kim, W. H. (2000) Allelotype analysis of intrahepatic cholangiocarcinoma. Mod. Pathol. 13, 627–631.PubMedCrossRefGoogle Scholar
  23. 23.
    Thibodeau, S. N., Bren, G., and Schaid, D. (1993) Microsatellite instability in cancer of the proximal colon. Science 260, 816–819.PubMedCrossRefGoogle Scholar
  24. 24.
    Aaltonen, L. A., Peltomaki, P., Leach, F. S., et al. (1993) Clues to the pathogenesis of familial colorectal cancer. Science 260, 812–816.PubMedCrossRefGoogle Scholar
  25. 25.
    Ionov, Y., Peinado, M. A., Malkhosyan, S., Shibata, D., and Perucho, M. (1993) Ubiquitous somatic mutations in simple repeated sequences reveal a new mechanism for colonic car-cinogenesis. Nature 363, 558–561.PubMedCrossRefGoogle Scholar
  26. 26.
    Peltomaki, P., Lothe, R. A., Aaltonen, L. A., et al. (1993) Microsatellite instability is associated with tumors that characterize the hereditary non-polyposis colorectal carcinoma syndrome. Cancer Res. 53, 5853–5855.PubMedGoogle Scholar
  27. 27.
    Lin, J. T., Wu, M. S., Shun, C. T., et al. (1995) Microsatellite instability in gastric carcinoma with special references to histopathology and cancer stages. Eur. J. Cancer 31A, 1879–1882.PubMedCrossRefGoogle Scholar
  28. 28.
    Leung, W. K., Kim, J. J., Kim, J. G., Graham, D. Y., and Sepulveda, A. R. (2000) Microsatellite instability in gastric intestinal metaplasia in patients with and without gastric cancer. Am. J. Pathol. 156, 537–543.PubMedCrossRefGoogle Scholar
  29. 29.
    Nakashima, H., Inoue, H., Mori, M., Ueo, H., Ikeda, M., and Akiyoshi, T. (1995) Microsatellite instability in Japanese gastric cancer. Cancer 75, 1503–1507.PubMedCrossRefGoogle Scholar
  30. 30.
    Renault, B., Calistri, D., Buonsanti, G., Nanni, O., Amadori, D., and Ranzani, G. N. (1996) Microsatellite instability and mutations of p53 and TGF-beta RII genes in gastric cancer. Hum. Genet. 98, 601–607.PubMedCrossRefGoogle Scholar
  31. 31.
    Rhyu, M. G., Park, W. S., and Meltzer, S. J. (1994) Microsatellite instability occurs frequently in human gastric carcinoma. Oncogene 9, 29–32.PubMedGoogle Scholar
  32. 32.
    Rugge, M., Shiao, Y. H., Guido, M., and Bovo, D. (1999) Microsatellite instability and gastric cancer subtypes. Hum. Pathol. 30, 108–109.PubMedCrossRefGoogle Scholar
  33. 33.
    Sepulveda, A. R., Santos, A. C., Yamaoka, Y., et al. (1999) Marked differences in the frequency of microsatellite instability in gastric cancer from different countries. Am. J. Gas-troenterol. 94, 3034–3038.CrossRefGoogle Scholar
  34. 34.
    Schneider, B. G., Pulitzer, D. R., Brown, R. D., et al. (1995) Allelic imbalance in gastric cancer: an affected site on chromosome arm 3p. Genes Chromosomes Cancer 13, 263–271.PubMedCrossRefGoogle Scholar
  35. 35.
    Semba, S., Yokozaki, H., Yasui, W., and Tahara, E. (1998) Frequent microsatellite instability and loss of heterozygosity in the region including BRCA1 (17q21) in young patients with gastric cancer. Int. J. Oncol. 12, 1245–1251.PubMedGoogle Scholar
  36. 36.
    Shiao, Y. H., Bovo, D., Guido, M., et al. (1999) Microsatellite instability and/or loss of heterozygosity in young gastric cancer patients in Italy. Int. J. Cancer 82, 59–62.PubMedCrossRefGoogle Scholar
  37. 37.
    Strickler, J. G., Zheng, J., Shu, Q., Burgart, L. J., Alberts, S. R., and Shibata, D. (1994) p53 mutations and microsatellite instability in sporadic gastric cancer: when guardians fail. Cancer Res. 54, 4750–4755.PubMedGoogle Scholar
  38. 38.
    Suzuki, H., Itoh, F., Toyota, M., et al. (1999) Distinct methylation pattern and microsatellite instability in sporadic gastric cancer. Int. J. Cancer 83, 309–313.PubMedCrossRefGoogle Scholar
  39. 39.
    Wang, Y., Shinmura, K., and Sugimura, H. (1997) [Microsatellite instability in gastric cancer with varied structure]. Rinsho Byori 45, 651–655.PubMedGoogle Scholar
  40. 40.
    Wang, Y., Ke, Y., Ning, T., et al. (1998) [Studies of microsatellite instability in Chinese gastric cancer tissues]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 15, 155–157.PubMedGoogle Scholar
  41. 41.
    Wu, M. S., Lee, C. W., Shun, C. T., et al. (1998) Clinicopathological significance of altered loci of replication error and microsatellite instability-associated mutations in gastric cancer. Cancer Res. 58, 1494–1497.PubMedGoogle Scholar
  42. 42.
    Nishimura, M., Furumoto, H., Kato, T., Kamada, M., and Aono, T. (2000) Microsatellite instability is a late event in the carcinogenesis of uterine cervical cancer. Gynecol. Oncol. 79, 201–206.PubMedCrossRefGoogle Scholar
  43. 43.
    Leach, F. S., Nicolaides, N. C., Papadopoulos, N., et al. (1993) Mutations of a mutS homolog in hereditary nonpolyposis colorectal cancer. Cell 75, 1215–1225.PubMedCrossRefGoogle Scholar
  44. 44.
    Fishel, R., Lescoe, M. K., Rao, M. R., et al. (1993) The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer. Cell 75, 1027–1038.PubMedCrossRefGoogle Scholar
  45. 45.
    Maehara, Y., Oda, S., and Sugimachi, K. (2001) The instability within: problems in current analyses of microsatellite instability. Mutat. Res. 461, 249–263.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2003

Authors and Affiliations

  • Jennifer J. Ascaño
    • 1
  • Steven M. Powell
    • 1
  1. 1.Division of Gastroenterology and HepatologyUniversity of Virginia Health SystemCharlottesville

Personalised recommendations