Introduction

The analysis of variants generated by exome sequencing (ES) of families with rare Mendelian diseases is a time-consuming, manual process that represents one barrier to applying the technology routinely. To address this issue, we have developed a software tool, VAR-MD (http://research.nhgri.nih.gov/software/var-md/), for analyzing the DNA sequence variants produced by human ES. VAR-MD generates a ranked list of variants using predicted pathogenicity, Mendelian inheritance models, genotype quality, and population variant frequency data. VAR-MD was tested using two previously solved data sets and one unsolved data set. In the solved cases, the correct variant was listed at the top of VAR-MD's variant ranking. In the unsolved case, the correct variant was highly ranked, allowing for subsequent identification and validation. We conclude that VAR-MD has the potential to enhance mutation identification using family based, annotated next generation sequencing data. Moreover, we predict an incremental advancement in software performance as the reference databases, such as Single Nucleotide Polymorphism Database and Human Gene Mutation Database, continue to improve.

Publications

  1. VAR-MD: a tool to analyze whole exome-genome variants in small human pedigrees with mendelian inheritance.
    Cite this
    Sincan M, Simeonov DR, Adams D, Markello TC, Pierson TM, Toro C, Gahl WA, Boerkoel CF, 2012-04-01 - Human mutation

Credits

  1. Murat Sincan
    Developer

    Medical Genetics Branch, National Human Genome Research Institute

  2. Dimitre R Simeonov
    Developer

  3. David Adams
    Developer

  4. Thomas C Markello
    Developer

  5. Tyler M Pierson
    Developer

  6. Camilo Toro
    Developer

  7. William A Gahl
    Developer

  8. Cornelius F Boerkoel
    Investigator

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Summary
AccessionBT000169
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByCornelius F Boerkoel