Shimmer: Detection of genetic alterations in tumors using next-generation sequence data

Bioinformatics

Volumn 29, Issue 12, 2013, Pages 1498-1503

  Hansen, Nancy F ^a   Gartner, Jared J ^a   Mei, Lan ^a   Samuels, Yardena ^b   Mullikin, James C ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; EXOME; GENETIC VARIABILITY; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METHODOLOGY; MUTATION; NEOPLASM; NUCLEOTIDE SEQUENCE; TUMOR CELL LINE;

ALGORITHMS; CELL LINE, TUMOR; DNA MUTATIONAL ANALYSIS; EXOME; GENETIC VARIATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MUTATION; NEOPLASMS; SOFTWARE;

EID: 84878846511     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt183     Document Type: Article

References (29)

1. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Soc. Stat. B, 57, 289-300.
2. Berger, M.F. et al. (2011) The genomic complexity of primary human prostate cancer. Nature, 470, 214-220.
3. Carter, S.L. et al. (2012) Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol., 30, 413-421.
4. Cibulskis, K. et al. (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol., 31, 213-219.
5. Danacek, P. et al. (2011) The variant call format and VCFtools. Bioinformatics, 27, 2156-2158.
6. Ding, J. et al. (2012a) Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinformatics, 28, 167-175.
7. Ding, L. et al. (2012b) Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature, 481, 506-510.
8. Forbes, S.A. et al. (2010) COSMIC (the Catalogue of SomaticMutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res., 38, D652-D657.
9. Gerstung, M. et al. (2012) Reliable detection of subclonal single-nucleotide variants in tumour cell populations. Nat. Commun., 3, 811.
10. Gui, Y. et al. (2011) Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder. Nat. Genet., 43, 875-878.
11. International Cancer Genome Consortium. (2010) International network of cancer genome projects. Nature, 464, 993-998.
12. Koboldt, D.C. et al. (2012) VarScan2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res., 22, 568-576.
13. Larson, D.E. et al. (2012) SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics, 28, 311-317.
14. Lee, W. et al. (2010) The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature, 465, 473-477.
15. Li, H. et al. (2009) The Sequence/Alignment Map format and Samtools. Bioinformatics, 25, 2078-2079.
16. Li, H. (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics, 27, 2987-2993.
17. Noble, W.S. (2009) How does multiple testing correction work Nat. Biotechnol., 27, 1135-1137.
18. Pleasance, E. et al. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, 463, 191-196.
19. Roth, A. et al. (2012) JoinSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics, 28, 907-913.
20. Saunders, C.T. et al. (2012) Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics, 28, 1811-1817.
21. Shah, S.P. et al. (2009) Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature, 461, 809-813.
22. Stark, M.S. et al. (2012) Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing. Nat. Genet., 44, 165-169.
23. Teer, J.K. et al. (2010) Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res., 20, 1420-1431.
24. Teer, J.K. et al. (2012) VarSifter: visualizing and analyzing exome-scale sequence variation data on a desktop computer. Bioinformatics, 28, 599-600.
25. The International HapMap Consortium. (2003) The InternationalHapMap Project. Nature, 426, 789-796.
26. Wang, K. et al. (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res., 38, e164.
27. Wei, X. et al. (2011) Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nat. Genet., 43, 442-446.
28. Yang, H. et al. (2011) Antitumor activity of BRAF inhibitor Vemurafenib in preclinical models of BRAF-mutant colorectal cancer. Cancer Res., 72, 779-789.
29. Zhang, H. et al. (2007) ErbB receptors: from oncogenes to targeted cancer therapies. J. Clin. Invest., 117, 2051-2058.