Combining calls from multiple somatic mutation-callers

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Kim, Su Y ^a   Jacob, Laurent ^b   Speed, Terence P ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITÉ LYON 1   (France)

^c UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Cancer genome; Combining calls; Somatic mutation calling; Stacking

Indexed keywords

GENES;

CANCER GENOME; COMBINING CALLS; MUTATION ANALYSIS; SOMATIC MUTATION; SOMATIC MUTATION-CALLING; STACKING; STATISTICAL APPROACH; STATISTICAL MODELING;

DISEASES;

ARTICLE; ENDOMETRIUM TUMOR; FEMALE; GENETICS; GENOME; GENOMICS; HUMAN; METHODOLOGY; MUTATION; NUCLEOTIDE SEQUENCE; STATISTICAL MODEL;

DNA MUTATIONAL ANALYSIS; ENDOMETRIAL NEOPLASMS; FEMALE; GENOME; GENOMICS; HUMANS; LOGISTIC MODELS; MODELS, STATISTICAL; MUTATION;

EID: 84901589136     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-154     Document Type: Article

References (15)

1. Hansen NF, Gartner JJ, Mei L, Samuels Y, Mullikin JC. Shimmer: detection of genetic alterations in tumors using next-generation sequence data. Bioinformatics 2013, 29(12):1498-1503. 10.1093/bioinformatics/btt183, 23620360.
2. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 2013, 31(3):213-219. 10.1038/nbt.2514, 3833702, 23396013.
3. Saunders CT, Wong WS, Swamy S, Becq J, Murray LJ, Cheetham RK. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 2012, 28(14):1811-1817. 10.1093/bioinformatics/bts271, 22581179.
4. Ding J, Bashashati A, Roth A, Oloumi A, Tse K, Zeng T, Haffari G, Hirst M, Marra MA, Condon A, Aparicio S, Shah SP. Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. Bioinformatics 2012, 28(2):167-175. 10.1093/bioinformatics/btr629, 3259434, 22084253.
5. Roth A, Ding J, Morin R, Crisan A, Ha G, Giuliany R, Bashashati A, Hirst M, Turashvili G, Oloumi A, Marra MA, Aparicio S, Shah SP. JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics 2012, 28(7):907-913. 10.1093/bioinformatics/bts053, 3315723, 22285562.
6. Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics 2012, 28(3):311-317. 10.1093/bioinformatics/btr665, 3268238, 22155872.
7. Lower M, Renard BY, de Graaf J, Wagner M, Paret C, Kneip C, Tureci O, Diken M, Britten C, Kreiter S, Koslowski M, Castle JC, Sahin U. Confidence-based somatic mutation evaluation and prioritization. PLoS Comput Biol 2012, 8(9):1002714.
8. Hastie T, Tibshirani R, Friedman J. The Elements of Statistical Learning 2009, New York: Springer.
9. Breiman L. Stacked regressions. Mach Learn 1996, 24(1):49-64.
10. The Cancer Genome Atlas Research Network Integrated genomic characterization of endometrial carcinoma. Nature 2013, 497(7447):67-73. 10.1038/nature12113, 3704730, 23636398, The Cancer Genome Atlas Research Network.
11. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
12. Wolpert DH. Stacked generalization. Neural Netw 1992, 5:241-259.
13. Sill J, Takács G, Mackey L, Lin D. Feature-weighted linear stacking. CoRR 2009, abs/0911.0460. [http://arxiv.org/abs/0911.0460].
14. Tibshirani R. Regression shrinkage and selection via the lasso. J R Stat Soc B 1996, 58(1):267-288.
15. Friedman J, Hastie T, Tibshirani R. Regularization paths for generalized linear models via coordinate descent. J Stat Softw 2010, 33(1):1-22. 2929880, 20808728.