title: The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.
abstract: Rapid development of next generation sequencing technology has enabled the identification of genomic alterations from short sequencing reads. There are a number of software pipelines available for calling single nucleotide variants from genomic DNA but, no comprehensive pipelines to identify, annotate and prioritize expressed SNVs (eSNVs) from non-directional paired-end RNA-Seq data. We have developed the eSNV-Detect, a novel computational system, which utilizes data from multiple aligners to call, even at low read depths, and rank variants from RNA-Seq. Multi-platform comparisons with the eSNV-Detect variant candidates were performed. The method was first applied to RNA-Seq from a lymphoblastoid cell-line, achieving 99.7% precision and 91.0% sensitivity in the expressed SNPs for the matching HumanOmni2.5 BeadChip data. Comparison of RNA-Seq eSNV candidates from 25 ER+ breast tumors from The Cancer Genome Atlas (TCGA) project with whole exome coding data showed 90.6-96.8% precision and 91.6-95.7% sensitivity. Contrasting single-cell mRNA-Seq variants with matching traditional multicellular RNA-Seq data for the MD-MB231 breast cancer cell-line delineated variant heterogeneity among the single-cells. Further, Sanger sequencing validation was performed for an ER+ breast tumor with paired normal adjacent tissue validating 29 out of 31 candidate eSNVs. The source code and user manuals of the eSNV-Detect pipeline for Sun Grid Engine and virtual machine are available at http://bioinformaticstools.mayo.edu/research/esnv-detect/.
authors.affiliation: Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA.
authors.forename: Xiaojia
authors.initials: X
authors.lastname: Tang
authors.affiliation: Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA.
authors.forename: Saurabh
authors.initials: S
authors.lastname: Baheti
authors.affiliation: Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA.
authors.forename: Khader
authors.initials: K
authors.lastname: Shameer
authors.affiliation: Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Thompson
authors.affiliation: Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
authors.forename: Quin
authors.initials: Q
authors.lastname: Wills
authors.affiliation: Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
authors.forename: Nifang
authors.initials: N
authors.lastname: Niu
authors.affiliation: Fluidigm Corporation, South San Francisco, CA 94080, USA.
authors.forename: Ilona N
authors.initials: IN
authors.lastname: Holcomb
authors.affiliation: Fluidigm Corporation, South San Francisco, CA 94080, USA.
authors.forename: Stephane C
authors.initials: SC
authors.lastname: Boutet
authors.affiliation: Fluidigm Corporation, South San Francisco, CA 94080, USA.
authors.forename: Ramesh
authors.initials: R
authors.lastname: Ramakrishnan
authors.affiliation: Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Kachergus
authors.affiliation: Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA.
authors.forename: Jean-Pierre A
authors.initials: JP
authors.lastname: Kocher
authors.affiliation: Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Weinshilboum
authors.affiliation: Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
authors.forename: Liewei
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA Kalari.Krishna@mayo.edu.
authors.forename: E Aubrey
authors.initials: EA
authors.lastname: Thompson
authors.affiliation: Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA Kalari.Krishna@mayo.edu.
authors.forename: Krishna R
authors.initials: KR
authors.lastname: Kalari
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics; D002460:Cell Line; D045744:Cell Line, Tumor; D059472:Exome; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D014644:Genetic Variation; D006801:Humans; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods*; D059010:Single-Cell Analysis; D012984:Software