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PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

Amit G Deshwar, Shankar Vembu, Christina K Yung and 3 more

Genome Biology · 2015 · CC BY

Abstract

Electronic supplementary material. The online version of this article (doi:10.1186/s13059-015-0602-8) contains supplementary material, which is available to authorized users.

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References 49

1.
Nowell PC. The clonal evolution of tumor cell populations. Science. 1976;194:23-8.
Not in our library10.1126/science.959840
2.
Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. New Engl J Med. 2012;366:883-92.
Not in our library10.1056/nejmoa1113205
3.
Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing. · 2014
Not checked
4.
Hanahan D, Weinberg RA. The hallmarks of cancer. Cell. 2000;100:57-70.
Not in our library10.1016/s0092-8674(00)81683-9
5.
Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144:646-74.
Not in our library10.1016/j.cell.2011.02.013
6.
Aparicio S, Caldas C. The implications of clonal genome evolution for cancer medicine. New Engl J Med. 2013;368:842-51.
Not in our library10.1056/nejmra1204892
7.
Bedard PL, Hansen AR, Ratain MJ, Siu LL. Tumour heterogeneity in the clinic. Nature. 2013;501:355-64.
Not in our library10.1038/nature12627
8.
Mullighan CG, Phillips LA, Su X, Ma J, Miller CB, Shurtleff SA, et al. Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia. Science. 2008;322:1377-80.
Not in our library10.1126/science.1164266
9.
Navin NE, Hicks J. Tracing the tumor lineage. Mol Oncol. 2010;4:267-83.
Not in our library10.1016/j.molonc.2010.04.010
10.
Marusyk A, Polyak K. Tumor heterogeneity: causes and consequences. Biochimica et Biophysica Acta. 2010;1805:105-17.
Not in our library10.1016/j.bbcan.2009.11.002
11.
Schuh A, Becq J, Humphray S, Alexa A, Burns A, Clifford R, et al. Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns. Blood. 2012;120:4191-6.
Not in our library10.1182/blood-2012-05-433540
12.
Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012;486:617-56.
Not in our library10.1038/nature10933
13.
Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, et al. Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol. 2012;30:413-21.
Not in our library10.1038/nbt.2203
14.
Landau DA, Carter SL, Stojanov P, McKenna A, Stevenson K, Lawrence MS, et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell. 2013;152:714-26.
Not in our library10.1016/j.cell.2013.01.019
15.
THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data · 2013
No notice
16.
Strino F, Parisi F, Micsinai M, Kluger Y. TrAp: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Res. 2013;41:e165.
Not in our library10.1093/nar/gkt641
17.
Inferring clonal evolution of tumors from single nucleotide somatic mutations · 2014
No notice
18.
Roth A, Khattra J, Yap D, Wan A, Laks E, Biele J, et al. PyClone: statistical inference of clonal population structure in cancer. Nat Methods. 2014;11:396-98.
Not in our library10.1038/nmeth.2883
19.
EXPANDS: expanding ploidy and allele frequency on nested subpopulations · 2013
No notice
20.
Chen M, Gunel M, Zhao H. SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data. PloS One. 2013;8:e78143.
Not in our library10.1371/journal.pone.0078143
21.
Larson NB, Fridley BL. PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data. Bioinformatics. 2013;29:1888-9.
Not in our library10.1093/bioinformatics/btt293
22.
Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, Ellrott K, et al. The cancer genome atlas pan-cancer analysis project. Nat Genet. 2013;45:1113-20.
Not in our library10.1038/ng.2764
23.
Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012;481:506-10.
Not in our library10.1038/nature10738
24.
Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, et al. Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol. 2012;30:413-21.
Not in our library10.1038/nbt.2203
25.
Gusnanto A, Wood HM, Pawitan Y, Rabbitts P, Berri S. Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. Bioinformatics. 2012;28:40-7.
Not in our library10.1093/bioinformatics/btr593
26.
The Life History of 21 Breast Cancers · 2012
Corrected
27.
Fischer A, Vázquez-García I, Illingworth CJ, Mustonen V. High-definition reconstruction of clonal composition in cancer. Cell Reports. 2014;7:1740-52.
Not in our library10.1016/j.celrep.2014.04.055
28.
PhyloWGS. https://github.com/morrislab/phylowgs.
Not in our library
29.
Behjati S, Huch M, van Boxtel R, Karthaus W, Wedge DC, Tamuri AU, et al. Genome sequencing of normal cells reveals developmental lineages and mutational processes. Nature. 2014;513:422-5.
Not in our library10.1038/nature13448
30.
Burrell RA, McGranahan N, Bartek J, Swanton C. The causes and consequences of genetic heterogeneity in cancer evolution. Nature. 2013;501:338-45.
Not in our library10.1038/nature12625
31.
Klein CA. Selection and adaptation during metastatic cancer progression. Nature. 2013;501:365-72.
Not in our library10.1038/nature12628
32.
SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution · 2014
No notice
33.
Hajirasouliha I, Mahmoody A, Raphael BJ. A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. Bioinformatics. 2014;30:78-86.
Not in our library10.1093/bioinformatics/btu284
34.
Kimura M. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics. 1969;61:893.
Not in our library10.1093/genetics/61.4.893
35.
Hudson RR. Properties of a neutral allele model with intragenic recombination. Theor Popul Biol. 1983;23:183-201.
Not in our library10.1016/0040-5809(83)90013-8
36.
Zare H, Wang J, Hu A, Weber K, Smith J, Nickerson D, et al. Inferring clonal composition from multiple sections of a breast cancer. PLoS Comput Biol. 2014;10:e1003703.
Not in our library10.1371/journal.pcbi.1003703
37.
Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, et al. Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Nat Acad Sci. 2011;108:E1128-36.
Not in our library10.1073/pnas.1110574108
38.
TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data · 2014
No notice
39.
Miller JW, Harrison MT. A simple example of Dirichlet process mixture inconsistency for the number of components. In: Advances in neural information processing systems. 2013:199–206.
Not in our library
40.
Davis J, Goadrich M. The relationship between precision–recall and ROC curves. In: Proceedings of the 23rd International Conference on Machine Learning: 2006. p. 233–40.
Not in our library
41.
Ewing A. TCGA mutation/variation calling benchmark 4. 2013. https://cghub.ucsc.edu/datasets/benchmark_download.html.
Not in our library
42.
Institute TB. Picard: Java tools for manipulating BAM files. http://picard.sourceforge.net/.
Not in our library
43.
Li H, Durbin R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics. 2010;26:589-95.
Not in our library10.1093/bioinformatics/btp698
44.
Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31:213-9.
Not in our library10.1038/nbt.2514
45.
Saunders CT, Wong WS, Swamy S, Becq J, Murray LJ, Cheetham RK, et al. Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs. Bioinformatics. 2012;28:1811-7.
Not in our library10.1093/bioinformatics/bts271
46.
Adams RP, Ghahramani Z, Jordan MI. Tree-structured stick breaking for hierarchical data. In: Advances in neural information processing systems 23: 2010. p. 19–27.
Not in our library
47.
Hastings WK. Monte Carlo sampling methods using Markov chains and their applications. Biometrika. 1970;57:97-109.
Not in our library10.1093/biomet/57.1.97
48.
Plummer M, Best N, Cowles K, Vines K. CODA: convergence diagnosis and output analysis for MCMC. R News. 2006;6:7-11.
Not in our library
49.
Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, et al. Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nat Genet. 2014;46:318-9.
Not in our library10.1038/ng.2932

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