Reconstructing tumor phylogenies from heterogeneous single-cell data

Journal of Bioinformatics and Computational Biology

Volumn 5, Issue 2 A, 2007, Pages 407-427

  Pennington, Gregory ^a   Smith, Charles A ^b   Shackney, Stanley ^b   Schwartz, Russell ^c  

^a Carnegie Mellon University   (United States)

^b ALLEGHENY GENERAL HOSPITAL   (United States)

^c CARNEGIE MELLON UNIVERSITY   (United States)

Author keywords

Cancer; Expectation maximization; Markov chain Monte Carlo; Tree

Indexed keywords

EPIDERMAL GROWTH FACTOR RECEPTOR 2; PROTEIN P53;

ACCURACY; BREAST CANCER; BREAST CARCINOGENESIS; CANCER GENETICS; CELL ASSAY; COMPUTER PROGRAM; CONFERENCE PAPER; CONTROLLED STUDY; DISEASE COURSE; DRUG TARGETING; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION PROFILING; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR MECHANICS; PATHOPHYSIOLOGY; PHYLOGENY; PROGNOSIS; SYMPTOM; TUMOR GROWTH;

EID: 34347403659     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/s021972000700259x     Document Type: Conference Paper

References (31)

1. Eisen MB, Spellman PT, Brown PO, Botstein D, Cluster analysis and display of genome-wide expression patterns, Proc Natl Acad Sci USA 95:14863-14868, 1998.
2. Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeej M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES, Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring, Science 286:531-537, 1999.
3. Peron CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lønning PE, Børresen-Dale A-L, Brown PO, Botstein D, Molecular portraits of human breast tumors, Nature 406:747-752, 2000.
4. Ross DT, Scherf U, Eisen MB, Peron CM, Rees C, Spellman P, Iyer V, Jeffrey SS, van de Rijn M, Waltham M, Pergamenschikov A, Lee JCF, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO, Systematic variation in gene expression patterns in human cancer cell lines, Nat Genet 24:227-235, 2000.
5. Sørlie T, Perou CM, Tibshirani R, Aas T, Geisler S, Johnsen H, Hastie T, Eisen MB, van de Rijn M, Jeffrey SS, Thorsen T, Quist H, Matese JC, Brown PO, Botstein D, Lønning PE, Børresen-Dale A-L, Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications, Proc Natl Acad Sci USA 98(19):10869-10874, 2001.
6. van 't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AA, Mao M, Peterse HL, van der Kooy K, Marton MJ, Witteveen AT, Schreiber GJ, Kerkhoven RM, Roberts C, Linsley PS, Bernards R, Friend SH, Gene expression profiling predicts clinical outcome of breast cancer, Nature 415 484-485, 2002.
7. van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, Schreiber GJ, Peterse JL, Roberts C, Marton MJ, Parrish M, Atsma D, Witteveen A, Glas A, Delahaye L, van der Velde T, Bartelink H, Rodenhuis S, Rutgers ET, Friend SH, Bernards R, A gene-expression signature as a predictor of survival in breast cancer, N Engl J Med 347 1999-2009, 2002.
8. Valk PJM, Verhaak RGW, Beijen MA, Erpelinck CAJ, van Waalwijk can Doorn-Khosrovani SB, Boer JM, Beverloo HB, Moorhose MJ, van der Spek PJ, Löwenberg B, Delwel R, Prognostically useful gene-expression profiles in acute myeloid leukemia, N Engl J Med 350(16 :1617-1628, 2004.
9. Cunliffe HE, Ringnér M, Bilke S, Walker RL, Cheung JM, Chen Y, Meltzer PS, The gene expression response of breast cancer to growth regulators: Patterns and correlation with tumor expression profiles, Cancer Res 63:7158-7166, 2003.
10. Ayers M, Symmans WF, Stec J, Damokosh AL Clark E, Hess K, Lecocke M, Metivier J, Booser D, Ibrahim N, Valero V, Royce M, Arun B, Whitman G, Ross J, Sniege N, Hotoagyi GN, Pusztai L, Gene expression profiles predict complete pathologic response to neoadjuvant paclitaxel and fluorouracil, doxorubicin, and cyclophosphamide chemotherapy in breast cancer, J Clin Oncol 22(12):1-10, 2004.
11. Pegram MD, Konecny G, Slamon DJ, The molecular and cellular biology of Her-2/neu gene amplification/overexpression and the clinical development of herceptin (trastuzumab) therapy for breast cancer, Cancer Treat Res 103:57-75, 2000.
12. Nowell PC, The clonal evolution of tumor cell populations, Science 194:23-28, 1976.
13. Shackney SE, Silverman JF, Molecular evolutionary patterns in breast cancer, Adv Anal Pathology 10(5):278-290, 2003.
14. Ried T, Heselmeyer-Haddad K, Blegen H, Schrock E, Auer G, Genomic changes defining the genesis, progression, and malignancy potential of solid human tumors: A phenotype/genotype correlation, Genes Chromosomes Cancer 25(3):195-204, 1999.
15. Desper R, Khan J, Schaffer AA, Tumor classification using phylogenetic methods on expression data, J Theor Biol 228:477-496, 2004.
16. Shackney SE, Smith CA, Pollice A, Brown K, Day R, Julian T, Silverman JF, Intracellular patterns of Her-2/neu, ras, and ploidy abnormalities in primary human breast cancers predict postoperative clinical disease-free survival, Clin Cancer Res 10:3042-3052, 2004.
17. Shackney SE, Smith CA, Miller BW, Burholt DR, Murtha K, Giles HR, Ketterer DM, Pollice AA, Model for the genetic evolution of human solid tumors, Cancer Res 49:3344-3354, 1989.
18. Janocko LE, Brown KA, Smith CA, Gu LP, Pollice AA, Singh SG, Julian T, Wolmark N, Sweeney L, Silverman JF, Shackney SE, Distinctive patterns of Her-2/neu, c-myc, and cyclin D1 gene amplification by fluorescence in situ hybridization in primary human breast cancers, Cytometry 46(3):136-149, 2001.
19. Chu Y, Liu T, On the shortest arborescence of a directed graph, Sci Sinica 14:1386-1400, 1965.
20. Sinclair A. Improved bounds for mixing rates of Markov chains and multicommodity flow, Combin Probab Comput, 1:351-370, 1992.
21. Jerrum M, Sinclair A. The Markov chain Monte Carlo method: An approach to approximate counting and integration, in Hochbaum DS (ed.), Approximation Algorithms for NP-Hard Problems. PWS Publishing, Boston, pp. 482-520, 1996.
22. Shackney SE, Singh SG, Yakulis R, Smith CA, Pollice AA, Petruolo S, Waggoner A, Hartsock RJ, Aneuploidy in breast cancer: A fluorescence in situ hybridization study, Cytometry 22(4 :282-291, 1995.
23. Salmon DJ, Clark GM, Wong SG, Levin WJ, Ullrich A, McGuire WL, Human breast cancer: Correlation of relapse and survival with amplification of the Her-2/neu oncogene, Science 235:177-182, 1987.
24. van de Vijver M, van de Bersselaar R, Devilee P, Cornelisse C, Peterse J, Nusse R, Amplification of the neu (c-erbB-2) oncogene in human mammary tumors is relatively frequent and is often accompanied by amplification of the linked c-erbA oncogene, Mol Cell Biol 7 5):2019-2023, 1987.
25. Shackney SE, Shankey TV, Common patterns of genetic evolution in human solid tumors, Cytometry 29:1-27, 1997.
26. Nederlof PM, van der Flier S, Verwoerd NP, Vrolijk J, Raap AK, Tanke HJ, Quantification of fluorescence in situ hybridization signals by image cytometry, Cytometry 13(8):846-52, 1992.
27. Netten H, Young IT, van Vliet LJ, Tanke HJ, Vroljik H, Sloos WC, FISH and chips: Automation of fluorescent dot counting in interphase cell nuclei, Cytometry 28(1):1-10, 1997.
28. Kozubek M, Kozubek S, Lukasova E, Mareckova A, Bartova E, Skalnikova M, Jergova A, High-resolution cytometry of FISH dots in interphase cell nuclei, Cytometry 36(4): 279-93, 1999.
29. Kozubek M, Kozubek S, Lukasova E, Bartova E, Skalnikova M, Matula P, Matula P, Jirsova P, Cafourkova A, Koutna I, Combined confocal and wide-field high-resolution cytometry of fluorescent in situ hybridization-stained cells, Cytometry 45(1):1 12, 2001.
30. Winston JS, Ramanaryanan T, Levine E, Her-2/neu evaluation in breast cancer: Are we there yet? Am J Clin Pathol 121:S33-S49, 2004.
31. Pennington G, Smith CA, Shackney S, Schwartz R, Expectation-maximization method for reconstructing tumor phylogenies from single-cell data, in Markstein P, Xu Y (eds.), Proc Comput Syst Bioinform Conf, pp. 371-380, 2006.