An ensemble approach to accurately detect somatic mutations using SomaticSeq

Genome Biology

Volumn 16, Issue 1, 2015, Pages

  Fang, Li Tai ^a   Afshar, Pegah Tootoonchi ^b   Chhibber, Aparna ^a   Mohiyuddin, Marghoob ^a   Fan, Yu ^c   Mu, John C ^a   Gibeling, Greg ^a   Barr, Sharon ^a   Asadi, Narges Bani ^a   Gerstein, Mark B ^d   Koboldt, Daniel C ^e   Wang, Wenyi ^c   Wong, Wing H ^f   Lam, Hugo Y K ^a  

^a Bina Technologies Inc   (United States)

^b Stanford University   (United States)

^c UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^d YALE UNIVERSITY   (United States)

^e WASHINGTON UNIVERSITY   (United States)

^f STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; COMPUTER MODEL; DATA ANALYSIS SOFTWARE; DECISION TREE; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC VARIABILITY; INDEL MUTATION; MUTATIONAL ANALYSIS; PREDICTION; SENSITIVITY ANALYSIS; SOMATIC MUTATION; DNA MUTATIONAL ANALYSIS; GENETICS; HUMAN; MACHINE LEARNING; NEOPLASM; PROCEDURES; VALIDATION STUDY;

DNA MUTATIONAL ANALYSIS; HUMANS; INDEL MUTATION; MACHINE LEARNING; NEOPLASMS;

EID: 84942061527     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-015-0758-2     Document Type: Article

References (31)

1. Wang Q, Jia P, Li F, Chen H, Ji H, Hucks D, et al. Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers. Genome Med. 2013; 5:91. doi:10.1186/gm495.
2. Roberts ND, Kortschak RD, Parker WT, Schreiber AW, Branford S, Scott HS, et al. A comparative analysis of algorithms for somatic SNV detection in cancer. Bioinformatics. 2013; 29:2223-30. doi: 10.1093/bioinformatics/btt375 .
3. 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. doi: 10.1038/nbt.2514 .
4. Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics. 2012; 28:311-17. doi: 10.1093/bioinformatics/btr665 .
5. Roth A, Ding J, Morin R, Crisan A, Ha G, Giuliany R, et al. JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics. 2012; 28:907-13. doi: 10.1093/bioinformatics/bts053 .
6. Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012; 22:568-76. doi: 10.1101/gr.129684.111 .
7. Lai Z, Markovets A, Ahdesmaki M, Johnson J. VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research. In: AACR Annual Meeting. AACR: 2015.
8. Edmonson MN, Zhang J, Yan C, Finney RP, Meerzaman DM, Buetow KH. Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. Bioinformatics. 2011; 27:865-6. doi: 10.1093/bioinformatics/btr032 .
9. Goode DL, Hunter SM, Doyle MA, Ma T, Rowley SM, Choong D, et al. A simple consensus approach improves somatic mutation prediction accuracy. Genome Med. 2013; 5:90. doi: 10.1186/gm494 .
10. Rashid M, Robles-Espinoza CD, Rust AG, Adams DJ. Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes. Bioinformatics. 2013; 29:2208-10. doi: 10.1093/bioinformatics/btt371 .
11. Kim SY, Jacob L, Speed TP. Combining calls from multiple somatic mutation-callers. BMC Bioinformatics. 2014; 15:154. doi: 10.1186/1471-2105-15-154 .
12. Banerji S, Cibulskis K, Rangel-Escareno C, Brown KK, Carter SL, Frederick AM, et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature. 2012; 486:405-9. doi: 10.1038/nature11154 .
13. Mark Culp KJ, Michailides G. ada: an R package for stochastic boosting. J Stat Softw. 2006; 17:9.
14. SomaticSeq project. http://bioinform.github.io/somaticseq/
15. SomaticSeq source code. https://github.com/bioinform/somaticseq/
16. SomaticSeq version 1.0. https://github.com/bioinform/somaticseq/releases/tag/1.0
17. Data description. http://bioinform.github.io/somaticseq/data.html
18. Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, et al.Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nat Methods. 2015; 12:623-30. doi: 10.1038/nmeth.3407 .
19. DREAM Challenges. http://dreamchallenges.org .
20. Morse HG, Moore GE. Cytogenetic homogeneity in eight independent sites in a case of malignant melanoma. Cancer Genet Cytogenet. 1993; 69:108-12.
21. Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, Humphray SJ, Greenman CD, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 2010; 463:191-6. doi: 10.1038/nature08658 .
22. Puente XS, Pinyol M, Quesada V, Conde L, Ordóñez GR, Villamor N, et al.Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature. 2011; 475:101-5. doi: 10.1038/nature10113 .
23. Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014; 46:310-15. doi: 10.1038/ng.2892 .
24. Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al.A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012; 6:80-92. doi: 10.4161/fly.19695 .
25. Liu X, Jian X, Boerwinkle E. dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum Mutat. 2013; 34:2393-402. doi: 10.1002/humu.22376 .
26. Josephidou M, Lynch AG, Tavaré S. multiSNV: a probabilistic approach for improving detection of somatic point mutations from multiple related tumour samples. Nucleic Acids Res. 2015; 43:61. doi: 10.1093/nar/gkv135 .
27. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al.DbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001; 29:308-11.
28. Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, et al.The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer. 2004; 91:355-8. doi: 10.1038/sj.bjc.6601894 .
29. Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, Del Angel G, Levy-Moonshine A, et al.From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. In: Current protocols in bioinformatics. Unit 11.10: 2013. doi: 10.1002/0471250953.bi1110s43 .
30. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al.The sequence alignment/map format and SAMtools. Bioinformatics. 2009; 25:2078-9.
31. Araten DJ, Golde DW, Zhang RH, Thaler HT, Gargiulo L, Notaro R, et al.A quantitative measurement of the human somatic mutation rate. Cancer Res. 2005; 65:8111-17. doi: 10.1158/0008-5472.CAN-04-1198 .