A comparative analysis of algorithms for somatic SNV detection in cancer

Bioinformatics

Volumn 29, Issue 18, 2013, Pages 2223-2230

  Roberts, Nicola D ^a,b   Kortschak, R Daniel ^a   Parker, Wendy T ^b   Schreiber, Andreas W ^a,b   Branford, Susan ^a,b   Scott, Hamish S ^a,b   Glonek, Garique ^a   Adelson, David L ^a,b  

^a UNIVERSITY OF ADELAIDE   (Australia)

^b CENTRE FOR CANCER BIOLOGY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPARATIVE STUDY; COMPUTER PROGRAM; DNA SEQUENCE; EXOME; GENETICS; GENOTYPING TECHNIQUE; HUMAN; MUTATION; NEOPLASM;

ALGORITHMS; EXOME; GENOTYPING TECHNIQUES; HUMANS; MUTATION; NEOPLASMS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84883479141     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt375     Document Type: Review

References (19)

1. Cibulskis,K. et al. (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotech., 31, 213-219.
2. Ding,L. et al. (2010) Analysis of next-generation genomic data in cancer: Accomplishments and challenges. Hum. Mol. Genet., 19, R188-R196.
3. Dohm,J.C. et al. (2008) Substantial biases in ultra-short read data sets from highthroughput DNA sequencing. Nucleic Acids Res., 36, e105.
4. Gundry,M. and Vijg,J. (2012) Direct mutation analysis by high-throughput sequencing: From germline to low-abundant, somatic variants. Mutat. Res., 729, 1-15.
5. Koboldt,D.C. et al. (2009) VarScan: Variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics, 25, 2283-2285.
6. Koboldt,D. et al. (2012) VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res., 22, 568-576.
7. Larson,D.E. et al. (2012) SomaticSniper: Identification of somatic point mutations in whole genome sequencing data. Bioinformatics, 28, 311-317.
8. Lee,A.J. and Swanton,C. (2012) Tumour heterogeneity and drug resistance: Personalising cancer medicine through functional genomics. Biochem. Pharmacol., 83, 1013-1020.
9. Liu,S. et al. (2002) Genetic instability favoring transversions associated with ErbB2- induced mammary tumorigenesis. Proc. Natl Acad. Sci. USA, 99, 3770-3775.
10. Loeb,L.A. (2011) Human cancers express mutator phenotypes: Origin, consequences and targeting. Nat. Rev. Cancer, 11, 450-457.
11. Meacham,F. et al. (2011) Identification and correction of systematic error in highthroughput sequence data. BMC Bioinformatics, 12, 451.
12. Meyerson,M. et al. (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet., 11, 685-696.
13. Nakamura,K. et al. (2011) Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res., 39, e90.
14. Oki,E. et al. (2009) The difference in p53 mutations between cancers of the upper and lower gastrointestinal tract. Digestion, 79, 33-39.
15. Pleasance,E.D. et al. (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, 463, 191-196.
16. Roth,A. et al. (2012) JointSNVMix: A probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics, 28, 907-913.
17. Salk,J.J. et al. (2010) Mutational heterogeneity in human cancers: Origin and consequences. Annu. Rev. Pathol., 5, 51-75.
18. Saunders,C.T. et al. (2012) Strelka: Accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics, 28, 1811-1817.
19. Yang,Z. et al. (2003) Likelihood models of somatic mutation and codon substitution in cancer genes. Genetics, 165, 695-705.