An analysis of exome sequencing for diagnostic testing of the genes associated with muscle disease and spastic paraplegia

Authors

  • Cristina Dias,

    1. Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
    2. Child and Family Research Institute, Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
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    • These authors contributed equally.

  • Murat Sincan,

    1. NIH Undiagnosed Diseases Program and NHGRI, National Institutes of Health, Bethesda, Maryland
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    • These authors contributed equally.

  • Praveen F. Cherukuri,

    1. NIH Undiagnosed Diseases Program and NHGRI, National Institutes of Health, Bethesda, Maryland
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    • These authors contributed equally.

  • Rosemarie Rupps,

    1. Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
    2. Child and Family Research Institute, Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
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  • Yan Huang,

    1. NIH Undiagnosed Diseases Program and NHGRI, National Institutes of Health, Bethesda, Maryland
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  • Hannah Briemberg,

    1. Division of Neurology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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  • Kathryn Selby,

    1. Division of Pediatric Neurology, Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
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  • James C. Mullikin,

    1. NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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    • For the NISC Comparative Sequencing Program

  • Thomas C. Markello,

    1. NIH Undiagnosed Diseases Program and NHGRI, National Institutes of Health, Bethesda, Maryland
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  • David R. Adams,

    1. NIH Undiagnosed Diseases Program and NHGRI, National Institutes of Health, Bethesda, Maryland
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  • William A. Gahl,

    1. NIH Undiagnosed Diseases Program and NHGRI, National Institutes of Health, Bethesda, Maryland
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  • Cornelius F. Boerkoel

    Corresponding author
    1. Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
    2. Child and Family Research Institute, Children's and Women's Health Centre of British Columbia, Vancouver, British Columbia, Canada
    3. NIH Undiagnosed Diseases Program and NHGRI, National Institutes of Health, Bethesda, Maryland
    • Cornelius F. Boerkoel, UDP Translational Laboratory, 9 Memorial Drive, Bldg 9, Rm 1E100, NHGRI, National Institutes of Health, Bethesda, MD 20892
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  • For the Focus on the NIH Undiagnosed Diseases Program

Abstract

In this study, we assess exome sequencing (ES) as a diagnostic alternative for genetically heterogeneous disorders. Because ES readily identified a previously reported homozygous mutation in the CAPN3 gene for an individual with an undiagnosed limb girdle muscular dystrophy, we evaluated ES as a generalizable clinical diagnostic tool by assessing the targeting efficiency and sequencing coverage of 88 genes associated with muscle disease (MD) and spastic paraplegia (SPG). We used three exome-capture kits on 125 individuals. Exons constituting each gene were defined using the UCSC and CCDS databases. The three exome-capture kits targeted 47–92% of bases within the UCSC-defined exons and 97–99% of bases within the CCDS-defined exons. An average of 61.2–99.5% and 19.1–99.5% of targeted bases per gene were sequenced to 20X coverage within the CCDS-defined MD and SPG coding exons, respectively. Greater than 95–99% of targeted known mutation positions were sequenced to ≥1X coverage and 55–87% to ≥20X coverage in every exome. We conclude, therefore, that ES is a rapid and efficient first-tier method to screen for mutations, particularly within the CCDS annotated exons, although its application requires disclosure of the extent of coverage for each targeted gene and supplementation with second-tier Sanger sequencing for full coverage. Hum Mutat 33:614–626, 2012. © 2012 Wiley Periodicals, Inc.

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