Modeling DNA methylation in a population of cancer cells

Statistical Applications in Genetics and Molecular Biology

Volumn 7, Issue 1, 2008, Pages

  Siegmund, Kimberly D ^a   Marjoram, Paul ^a   Shibata, Darryl ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

Approximate Bayesian computation; Gompertzian growth; Mathematical modeling

Indexed keywords

ARTICLE; BAYES THEOREM; CANCER CELL; CELL GROWTH; CLINICAL ARTICLE; COLORECTAL CANCER; CONTROLLED STUDY; DNA METHYLATION; GENE REPLICATION; HUMAN; HUMAN CELL; HUMAN TISSUE; MALE; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; ANIMAL; BIOLOGICAL MODEL; CELL TRANSFORMATION; CPG ISLAND; GENETIC EPIGENESIS; METABOLISM; NEOPLASM;

DNA;

ANIMALS; CELL TRANSFORMATION, NEOPLASTIC; CPG ISLANDS; DNA METHYLATION; DNA, NEOPLASM; EPIGENESIS, GENETIC; HUMANS; MODELS, BIOLOGICAL; NEOPLASMS;

EID: 46749159387     PISSN: None     EISSN: 15446115     Source Type: Journal    
DOI: 10.2202/1544-6115.1374     Document Type: Article

References (29)

1. Al-Hajj, M. and Clarke, M. F. (2004). Self-renewal and solid tumor stem cells. Oncogene 23, 7274-82.
2. Frommer, M., McDonald, L. E., Millar, D. S., Collis, C. M., Watt, F., Grigg, G. W., Molloy, P. L. and Paul, C. L. (1992). A Genomic Sequencing Protocol that Yields a Positive Display of 5-Methylcytosine Residues in Individual DNA Strands. PNAS 89, 1827-1831.
3. Fu, Y.-X. and Li, W.-H. (1997). Estimating the age of the common ancestor of a sample of DNA sequences. Molecular Biology and Evolution 14, 195-199.
4. Gilks, W. R., Richardson, S. and Spiegelhalter, D. J. Markov chain Monte Carlo in Practice (1996). Chapman & Hall, London.
5. Hill, R. P. and Perris, R. (2007). "Destemming" cancer stem cells. J Natl Cancer Inst 99, 1435-40.
6. Issa, J. P. (2000). CpG-island methylation in aging and cancer. Curr Top Microbiol Immunol 249, 101-18.
7. Jaenisch, R. and Bird, A. (2003). Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature Genetics 33 Suppl, 245-54.
8. Jordan, C. T., Guzman, M. L. and Noble, M. (2006). Cancer stem cells. New England Journal of Medicine 355, 1253-61.
9. Kelly, P. N., Dakic, A., Adams, J. M., Nutt, S. L. and Strasser, A. (2007). Tumor growth need not be driven by rare cancer stem cells. Science 317, 337.
10. Kern, S. E. and Shibata, D. (2007). The fuzzy math of solid tumor stem cells: a perspective. Cancer Res 67, 8985-8.
11. Kim, J. Y., Siegmund, K. D., Tavare, S. and Shibata, D. (2005a). Age-related human small intestine methylation: evidence for stem cell niches. BMC Medicine 3, 10.
12. Kim, J. Y., Tavare, S. and Shibata, D. (2005b). Counting human somatic cell replications: methylation mirrors endometrial stem cell divisions. Proceedings of the National Academy of Sciences U S A 102, 17739-44.
13. Liu, J. S. Monte Carlo Sampling Strategies in Scientific Computing (2001). Springer, New York.
14. Marjoram, P. and Tavaré, S. (2006). Modern computational approaches for analysing molecular genetic variation data. Nature Reviews Genetics 7, 759-70.
15. Norton, L. (1988). A Gompertzian model of human breast cancer growth. Cancer Res 48, 7067-71.
16. Nowell, P. C. (1976). The clonal evolution of tumor cell populations. Science 194, 23-8.
17. Padhukasahasram, B., Marjoram, P. and Nordborg, M. (2004). Estimating the rate of gene conversion on human chromosome 21. American Journal of Human Genetics 75, 386-97.
18. Polyak, K. and Hahn, W. C. (2006). Roots and stems: stem cells in cancer. Nature Medicine 12, 296-300.
19. Reya, T., Morrison, S. J., Clarke, M. F. and Weissman, I. L. (2001). Stem cells, cancer, and cancer stem cells. Nature 414, 105-11.
20. Ripley, B. D. Stochastic simulation (1982). John Wiley & Sons, Inc., New York.
21. Shibata, D. and Tavare, S. (2006). Counting divisions in a human somatic cell tree: how, what and why? Cell Cycle 5, 610-4.
22. Skilling, J. Nested sampling for Bayesian computations In Bayesian Statistics 8: Proceedings of the English Valencia Inernational Meeting (2007). Bernardo, J. M., Bayarri, M. J. , Berger, J. O., Dawid, A. P., Heckerman, D., Smith, A. F. M. and West, M. (eds.) Oxford University Press.
23. Slatkin, M. and Hudson, R. R. (1991). Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129, 555-62.
24. SPLUS, http://www.insightful.com/products/default.asp.
25. Steele, G. G. Growth kinetics of tumors (1977). Clarendon Press, Oxford.
26. Tavaré, S., Balding, D. J., Griffiths, R. C. and Donnelly, P. (1997). Inferring coalescence times for molecular sequence data. Genetics 145, 505-518.
27. Weiss, G. and Haeseler, A. v. (1998). Inference of population history using a likelihood approach. Genetics 149, 1539-1546.
28. Wood, L. D., Parsons, D. W., Jones, S., Lin, J., Sjoblom, T., Leary, R. J., Shen, D., Boca, S. M., Barber, T., Ptak, J., Silliman, N., Szabo, S., Dezso, Z., Ustyanksky, V., Nikolskaya, T., Nikolsky, Y., Karchin, R., Wilson, P. A., Kaminker, J. S., Zhang, Z., Croshaw, R., Willis, J., Dawson, D., Shipitsin, M., Willson, J. K., Sukumar, S., Polyak, K., Park, B. H., Pethiyagoda, C. L., Pant, P. V., Ballinger, D. G., Sparks, A. B., Hartigan, J., Smith, D. R., Suh, E., Papadopoulos, N., Buckhaults, P., Markowitz, S. D., Parmigiani, G., Kinzler, K. W., Velculescu, V. E. and Vogelstein, B. (2007). The genomic landscapes of human breast and colorectal cancers. Science 318, 1108-13.
29. Yatabe, Y., Tavare, S. and Shibata, D. (2001). Investigating stem cells in human colon by using methylation patterns. Proceedings of the National Academy of Sciences U S A 98, 10839-44.