Introduction

Forward genetic screens in model organisms are vital for identifying novel genes essential for developmental or disease processes. One drawback of these screens is the labor-intensive and sometimes inconclusive process of mapping the causative mutation. To leverage high-throughput techniques to improve this mapping process, we have developed a Mutation Mapping Analysis Pipeline for Pooled RNA-seq (MMAPPR) that works without parental strain information or requiring a preexisting SNP map of the organism, and adapts to differential recombination frequencies across the genome. MMAPPR accommodates the considerable amount of noise in RNA-seq data sets, calculates allelic frequency by Euclidean distance followed by Loess regression analysis, identifies the region where the mutation lies, and generates a list of putative coding region mutations in the linked genomic segment. MMAPPR can exploit RNA-seq data sets from isolated tissues or whole organisms that are used for gene expression and transcriptome analysis in novel mutants. We tested MMAPPR on two known mutant lines in zebrafish, nkx2.5 and tbx1, and used it to map two novel ENU-induced cardiovascular mutants, with mutations found in the ctr9 and cds2 genes. MMAPPR can be directly applied to other model organisms, such as Drosophila and Caenorhabditis elegans, that are amenable to both forward genetic screens and pooled RNA-seq experiments. Thus, MMAPPR is a rapid, cost-efficient, and highly automated pipeline, available to perform mutant mapping in any organism with a well-assembled genome.

Publications

  1. MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq.
    Cite this
    Hill JT, Demarest BL, Bisgrove BW, Gorsi B, Su YC, Yost HJ, 2013-04-01 - Genome research

Credits

  1. Jonathon T Hill
    Developer

    Department of Neurobiology and Anatomy, University of Utah Molecular Medicine Program, United States of America

  2. Bradley L Demarest
    Developer

  3. Brent W Bisgrove
    Developer

  4. Bushra Gorsi
    Developer

  5. Yi-Chu Su
    Developer

  6. H Joseph Yost
    Investigator

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Summary
AccessionBT001887
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByH Joseph Yost