Comparing Algorithms That Reconstruct Cell Lineage Trees Utilizing Information on Microsatellite Mutations

PLoS Computational Biology

Volumn 9, Issue 11, 2013, Pages

  Chapal Ilani, Noa ^a   Maruvka, Yosef E ^a   Spiro, Adam ^a   Reizel, Yitzhak ^a   Adar, Rivka ^a   Shlush, Liran I ^b   Shapiro, Ehud ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; CELL CULTURE; CELL PROLIFERATION; DNA SEQUENCES; FORESTRY; GENES; GENOME; MAMMALS; STEM CELLS;

CELL LINEAGE; CELLULARS; COMPARING ALGORITHM; DIRECTED EDGES; FERTILIZED EGGS; GENOMICS; INDIVIDUAL CELLS; MICROSATELLITES; PAST AND PRESENT; SOMATIC MUTATION;

TREES (MATHEMATICS);

ALGORITHM; ANIMAL CELL; ARTICLE; CELL DIVISION; CELL ISOLATION; CELL LINEAGE; CLUSTER ANALYSIS; GENOME; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; MICROSATELLITE MARKER; MOUSE; NEIGHBOR JOINING METHOD; NONHUMAN; PHYLOGENETIC TREE CONSTRUCTION METHOD; SOMATIC MUTATION; VALIDATION PROCESS;

MUS;

ALGORITHMS; ANIMALS; BONE MARROW CELLS; CELL LINEAGE; CELLS, CULTURED; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; FEMALE; HUMANS; MALE; MICE; MICE, TRANSGENIC; MICROSATELLITE REPEATS; MODELS, GENETIC; MUTATION; PHYLOGENY;

EID: 84888230291     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003297     Document Type: Article

References (47)

1. Frumkin D, Wasserstrom A, Kaplan S, Feige U, Shapiro E, (2005) Genomic variability within an organism exposes its cell lineage tree. PLoS Comput Biol 1: e50.
2. Sulston JE, Schierenberg E, White JG, Thomson JN, (1983) The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev Biol 100: 64-119.
3. Salipante SJ, Horwitz MS, (2006) Phylogenetic fate mapping. Proc Natl Acad Sci U S A 103: 5448-5453.
4. Salipante SJ, Horwitz MS, (2007) A phylogenetic approach to mapping cell fate. Curr Top Dev Biol 79: 157-184.
5. Frumkin D, Wasserstrom A, Itzkovitz S, Stern T, Harmelin A, et al. (2008) Cell lineage analysis of a mouse tumor. Cancer Res 68: 5924-5931.
6. Reizel Y, Chapal-Ilani N, Adar R, Itzkovitz S, Elbaz J, et al. (2011) Colon stem cell and crypt dynamics exposed by cell lineage reconstruction. PLoS Genet 7: e1002192.
7. Reizel Y, Itzkovitz S, Adar R, Elbaz J, Jinich A, et al. (2012) Cell lineage analysis of the Mammalian female germline. PLoS Genet 8: e1002477.
8. Segev E, Shefer G, Adar R, Chapal-Ilani N, Itzkovitz S, et al. (2011) Muscle-bound primordial stem cells give rise to myofiber-associated myogenic and non-myogenic progenitors. PLoS One 6: e25605.
9. Shlush LI, Chapal-Ilani N, Adar R, Pery N, Maruvka Y, et al. (2012) Cell lineage analysis of acute leukemia relapse uncovers the role of replication-rate heterogeneity and miscrosatellite instability. Blood.
10. Wasserstrom A, Adar R, Shefer G, Frumkin D, Itzkovitz S, et al. (2008) Reconstruction of cell lineage trees in mice. PLoS One 3: e1939.
11. Ellegren H, (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5: 435-445.
12. Payseur BA, Jing P, Haasl RJ, (2011) A genomic portrait of human microsatellite variation. Mol Biol Evol 28: 303-312.
13. Subramanian S, Mishra RK, Singh L, (2003) Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol 4: R13.
14. Wasserstrom A, Frumkin D, Adar R, Itzkovitz S, Stern T, et al. (2008) Estimating cell depth from somatic mutations. PLoS Comput Biol 4: e1000058.
15. Wei K, Kucherlapati R, Edelmann W, (2002) Mouse models for human DNA mismatch-repair gene defects. Trends Mol Med 8: 346-353.
16. Vilkki S, Tsao JL, Loukola A, Pöyhönen M, Vierimaa O, et al. (2001) Extensive somatic microsatellite mutations in normal human tissue. Cancer Res 61: 4541-4544.
17. Nachman MW, Crowell SL, (2000) Estimate of the mutation rate per nucleotide in humans. Genetics 156: 297-304.
18. Salipante SJ, Thompson JM, Horwitz MS, (2008) Phylogenetic fate mapping: theoretical and experimental studies applied to the development of mouse fibroblasts. Genetics 178: 967-977.
19. Salipante SJ, Kas A, McMonagle E, Horwitz MS, (2010) Phylogenetic analysis of developmental and postnatal mouse cell lineages. Evol Dev 12: 84-94.
20. Tsao JL, Tavaré S, Salovaara R, Jass JR, Aaltonen LA, et al. (1999) Colorectal adenoma and cancer divergence. Evidence of multilineage progression. Am J Pathol 154: 1815-1824.
21. Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, et al. (2012) Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 481: 506-510.
22. Carlson CA, Kas A, Kirkwood R, Hays LE, Preston BD, et al. (2012) Decoding cell lineage from acquired mutations using arbitrary deep sequencing. Nat Methods 9: 78-80.
23. Hou Y, Song L, Zhu P, Zhang B, Tao Y, et al. (2012) Single-cell exome sequencing and monoclonal evolution of a JAK2-negative myeloproliferative neoplasm. Cell 148: 873-885.
24. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, et al. (2011) Tumour evolution inferred by single-cell sequencing. Nature 472: 90-94.
25. Hong YJ, Marjoram P, Shibata D, Siegmund KD, (2010) Using DNA methylation patterns to infer tumor ancestry. PLoS One 5: e12002.
26. Siegmund KD, Marjoram P, Woo YJ, Tavaré S, Shibata D, (2009) Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers. Proc Natl Acad Sci U S A 106: 4828-4833.
27. Nicolas P, Kim KM, Shibata D, Tavaré S, (2007) The stem cell population of the human colon crypt: analysis via methylation patterns. PLoS Comput Biol 3: e28.
28. Gao F, Bailes E, Robertson DL, Chen YL, Rodenburg CM, et al. (1999) Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 397: 436-441.
29. Takezaki N, Nei M, (1996) Genetic distances and reconstruction of phylogenetic trees from microsatellite DNA. Genetics 144: 389-399.
30. Takezaki N, Nei M, (2008) Empirical tests of the reliability of phylogenetic trees constructed with microsatellite DNA. Genetics 178: 385-392.
31. Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
32. Sokal RR, Michener CD, (1958) A statistical method for evaluating systematic relationships. Univ Kans Sci Bull 38: 1409-1438.
33. Snir S, Rao S, (2010) Quartets MaxCut: A Divide and Conquer Quartets Algorithm. Ieee-Acm Transactions on Computational Biology and Bioinformatics 7: 704-718.
34. Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
35. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, et al. (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61: 539-542.
36. Beerli P, Felsenstein J, (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences of the United States of America 98: 4563-4568.
37. Wu CH, Drummond AJ, (2011) Joint inference of microsatellite mutation models, population history and genealogies using transdimensional Markov Chain Monte Carlo. Genetics 188: 151-164.
38. Wilson IJ, Weale ME, Balding DJ, (2003) Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities. Journal of the Royal Statistical Society Series a-Statistics in Society 166: 155-188.
39. Felsenstein J, (2004) Inferring phylogenies. Inferring phylogenies pp. i-xx.
40. Kuhner MK, Felsenstein J, (1994) Simulation Comparison of Phylogeny Algorithms Under Equal And Unequal Evolutionary Rates. Molecular Biology and Evolution 11: 459-468.
41. Snir S, Warnow T, Rao S, (2008) Short quartet puzzling: a new quartet-based phylogeny reconstruction algorithm. J Comput Biol 15: 91-103.
42. Ota T, Kimura M, (1973) A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genet Res 22: 201-204.
43. Ellegren H, (2000) Microsatellite mutations in the germline: implications for evolutionary inference. Trends Genet 16: 551-558.
44. Baker SM, Plug AW, Prolla TA, Bronner CE, Harris AC, et al. (1996) Involvement of mouse Mlh1 in DNA mismatch repair and meiotic crossing over. Nature Genetics 13: 336-342.
45. Frumkin D, Wasserstrom A, Itzkovitz S, Harmelin A, Rechavi G, et al. (2008) Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues. BMC Biotechnology pp. 17 (16 pp.).
46. Kumar G, Garnova E, Reagin M, Vidali A, (2008) Improved multiple displacement amplification with phi 29 DNA polymerase for genotyping of single human cells. Biotechniques 44: 879-+.
47. Graur D, Wen-Hsiung L (2000) Fundamental molecular evolution. Sinauer Associates.