title: An ensemble approach to accurately detect somatic mutations using SomaticSeq.
abstract: SomaticSeq is an accurate somatic mutation detection pipeline implementing a stochastic boosting algorithm to produce highly accurate somatic mutation calls for both single nucleotide variants and small insertions and deletions. The workflow currently incorporates five state-of-the-art somatic mutation callers, and extracts over 70 individual genomic and sequencing features for each candidate site. A training set is provided to an adaptively boosted decision tree learner to create a classifier for predicting mutation statuses. We validate our results with both synthetic and real data. We report that SomaticSeq is able to achieve better overall accuracy than any individual tool incorporated.
authors.affiliation: Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA. li\_tai.fang@bina.roche.com.
authors.forename: Li Tai
authors.initials: LT
authors.lastname: Fang
authors.affiliation: Department of Electrical Engineering, Stanford University, Stanford, 94305, CA, USA. pegahta@stanford.edu.
authors.forename: Pegah Tootoonchi
authors.initials: PT
authors.lastname: Afshar
authors.affiliation: Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA. aparna.chhibber@bina.roche.com.
authors.forename: Aparna
authors.initials: A
authors.lastname: Chhibber
authors.affiliation: Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA. marghoob.mohiyuddin@bina.roche.com.
authors.forename: Marghoob
authors.initials: M
authors.lastname: Mohiyuddin
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA. YFan1@mdanderson.org.
authors.forename: Yu
authors.initials: Y
authors.lastname: Fan
authors.affiliation: Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA. john.mu@bina.roche.com.
authors.forename: John C
authors.initials: JC
authors.lastname: Mu
authors.affiliation: Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA. greg.gibeling@bina.roche.com.
authors.forename: Greg
authors.initials: G
authors.lastname: Gibeling
authors.affiliation: Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA. sharon.barr@bina.roche.com.
authors.forename: Sharon
authors.initials: S
authors.lastname: Barr
authors.affiliation: Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA. narges.baniasadi@bina.roche.com.
authors.forename: Narges Bani
authors.initials: NB
authors.lastname: Asadi
authors.affiliation: Program in Computational Biology and Bioinformatics, Yale University, New Haven, 06520, CT, USA. mark.gerstein@yale.edu.
authors.forename: Mark B
authors.initials: MB
authors.lastname: Gerstein
authors.affiliation: The Genome Institute, Washington University in St Louis, St Louis, 63108, MO, USA. dkoboldt@genome.wustl.edu.
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Koboldt
authors.affiliation: Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA. wwang7@mdanderson.org.
authors.forename: Wenyi
authors.initials: W
authors.lastname: Wang
authors.affiliation: Department of Statistics, Stanford University, Stanford, 94305, CA, USA. whwong@stanford.edu.|Department of Health Research and Policy, Stanford University, Stanford, 94305, CA, USA. whwong@stanford.edu.
authors.forename: Wing H
authors.initials: WH
authors.lastname: Wong
authors.affiliation: Bina Technologies, Roche Sequencing, Redwood City, 94065, CA, USA. hugo.lam@bina.roche.com.
authors.forename: Hugo Y K
authors.initials: HY
authors.lastname: Lam
mesh_terms: D004252:DNA Mutational Analysis / Q000379:methods*; D006801:Humans; D054643:INDEL Mutation; D000069550:Machine Learning; D009369:Neoplasms / Q000235:genetics*