Abstract
Copy number variants are an underlying factor in human evolution and in many diseases, especially in cancer. Tumors generally contain cells with a varying number of gene copies, and the variance in the number of gene copies follows a pattern formed by an evolutionary process. The Fluorescence in situ hybridization (FISH) provides researchers a reliable technique to measure the copy numbers of preselected genes in a group of cells. Recently, Chowdhury et al. successfully modeled the progression of tumor progression using FISH copy number to the Rectilinear Steiner Minimum Tree (RSMT) problem, and proposed both exact and heuristic algorithms to reconstruct phylogenetic trees modeling the development of cancer cell patterns [1]. We proposed new heuristics to attack the RSMT problem, which is inspired by iterative approaches to approximate solutions to the Steiner tree in the “small phylogeny” problem [2,3]. Experimental results from both simulated and real tumor data show that our approach outperforms the previous heuristic algorithm in approximating better solutions for the RSMT problem.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Chowdhury, S.A., Shackney, S.E., Heselmeyer-Haddad, K., Ried, T., Schäffer, A.A., Schwartz, R.: Phylogenetic analysis of multiprobe fluorescence in situ hybridization data from tumor cell populations. Bioinformatics 29(13), 189–198 (2013)
Sankoff, D., Cedergren, R.J., Lapalme, G.: Frequency of insertion-deletion, transversion, and transition in the evolution of 5s ribosomal rna. Journal of Molecular Evolution 7(2), 133–149 (1976)
Blanchette, M., Bourque, G., Sankoff, D.: Breakpoint phylogenies. Genome Informatics 8, 25–34 (1997)
Futreal, P.A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., Stratton, M.R.: A census of human cancer genes. Nature Reviews Cancer 4(3), 177–183 (2004)
Yates, L.R., Campbell, P.J.: Evolution of the cancer genome. Nature Reviews Genetics 13(11), 795–806 (2012)
Baudis, M.: Genomic imbalances in 5918 malignant epithelial tumors: an explorative meta-analysis of chromosomal CGH data. BMC Cancer 7(1), 226 (2007)
Pleasance, E.D., Cheetham, R.K., Stephens, P.J., McBride, D.J., Humphray, S.J., Greenman, C.D., Varela, I., Lin, M.-L., Ordóñez, G.R., Bignell, G.R., et al.: A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463(7278), 191–196 (2009)
Martins, F.C., De, S., Almendro, V., Gönen, M., Park, S.Y., Blum, J.L., Herlihy, W., Ethington, G., Schnitt, S.J., Tung, N., et al.: Evolutionary pathways in BRCA1-associated breast tumors. Cancer Discovery 2(6), 503–511 (2012)
Navin, N., Krasnitz, A., Rodgers, L., Cook, K., Meth, J., Kendall, J., Riggs, M., Eberling, Y., Troge, J., Grubor, V., et al.: Inferring tumor progression from genomic heterogeneity. Genome Research 20(1), 68–80 (2010)
Cheng, Y.-K., Beroukhim, R., Levine, R.L., Mellinghoff, I.K., Holland, E.C., Michor, F.: A mathematical methodology for determining the temporal order of pathway alterations arising during gliomagenesis. PLOS Computational Biology 8(1), 1002337
Caldecott, K.W.: Single-strand break repair and genetic disease. Nature Reviews Genetics 9(8), 619–631 (2008)
Hastings, P., Lupski, J.R., Rosenberg, S.M., Ira, G.: Mechanisms of change in gene copy number. Nature Reviews Genetics 10(8), 551–564 (2009)
Cleaver, J.E., Lam, E.T., Revet, I.: Disorders of nucleotide excision repair: the genetic and molecular basis of heterogeneity. Nature Reviews Genetics 10(11), 756–768 (2009)
Langer-Safer, P.R., Levine, M., Ward, D.C.: Immunological method for mapping genes on drosophila polytene chromosomes. Proceedings of the National Academy of Sciences 79(14), 4381–4385 (1982)
Attolini, C.S.-O., Michor, F.: Evolutionary theory of cancer. Annals of the New York Academy of Sciences 1168(1), 23–51 (2009)
Greenman, C.D., Pleasance, E.D., Newman, S., Yang, F., Fu, B., Nik-Zainal, S., Jones, D., Lau, K.W., Carter, N., Edwards, P.A., et al.: Estimation of rearrangement phylogeny for cancer genomes. Genome Research 22(2), 346–361 (2012)
Shlush, L.I., Chapal-Ilani, N., Adar, R., Pery, N., Maruvka, Y., Spiro, A., Shouval, R., Rowe, J.M., Tzukerman, M., Bercovich, D., et al.: Cell lineage analysis of acute leukemia relapse uncovers the role of replication-rate heterogeneity and microsatellite instability. Blood 120(3), 603–612 (2012)
Pennington, G., Smith, C.A., Shackney, S., Schwartz, R.: Reconstructing tumor phylogenies from heterogeneous single-cell data. Journal of Bioinformatics and Computational Biology 5(02a), 407–427 (2007)
Fertin, G.: Combinatorics of Genome Rearrangements, pp. 133–149 (2009)
Garey, M.R., Johnson, D.S.: The rectilinear steiner tree problem is NP-complete. SIAM Journal on Applied Mathematics 32(4), 826–834 (1977)
Chowdhury, S.A., Shackney, S.E., Heselmeyer-Haddad, K., Ried, T., Schäffer, A.A., Schwartz, R.: Algorithms to model single gene, single chromosome, and whole genome copy number changes jointly in tumor phylogenetics. PLOS Computational Biology 10(7), 1003740 (2014)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Zhou, J., Lin, Y., Hoskins, W., Tang, J. (2015). An Iterative Approach for Phylogenetic Analysis of Tumor Progression Using FISH Copy Number. In: Harrison, R., Li, Y., Măndoiu, I. (eds) Bioinformatics Research and Applications. ISBRA 2015. Lecture Notes in Computer Science(), vol 9096. Springer, Cham. https://doi.org/10.1007/978-3-319-19048-8_34
Download citation
DOI: https://doi.org/10.1007/978-3-319-19048-8_34
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-19047-1
Online ISBN: 978-3-319-19048-8
eBook Packages: Computer ScienceComputer Science (R0)