title: Expanding genotype/phenotype of neuromuscular diseases by comprehensive target capture/NGS.
abstract: OBJECTIVE
  To establish and evaluate the effectiveness of a comprehensive next-generation sequencing (NGS) approach to simultaneously analyze all genes known to be responsible for the most clinically and genetically heterogeneous neuromuscular diseases (NMDs) involving spinal motoneurons, neuromuscular junctions, nerves, and muscles.
  
  
  METHODS
  All coding exons and at least 20 bp of flanking intronic sequences of 236 genes causing NMDs were enriched by using SeqCap EZ solution-based capture and enrichment method followed by massively parallel sequencing on Illumina HiSeq2000.
  
  
  RESULTS
  The target gene capture/deep sequencing provides an average coverage of ∼1,000× per nucleotide. Thirty-five unrelated NMD families (38 patients) with clinical and/or muscle pathologic diagnoses but without identified causative genetic defects were analyzed. Deleterious mutations were found in 29 families (83%). Definitive causative mutations were identified in 21 families (60%) and likely diagnoses were established in 8 families (23%). Six families were left without diagnosis due to uncertainty in phenotype/genotype correlation and/or unidentified causative genes. Using this comprehensive panel, we not only identified mutations in expected genes but also expanded phenotype/genotype among different subcategories of NMDs.
  
  
  CONCLUSIONS
  Target gene capture/deep sequencing approach can greatly improve the genetic diagnosis of NMDs. This study demonstrated the power of NGS in confirming and expanding clinical phenotypes/genotypes of the extremely heterogeneous NMDs. Confirmed molecular diagnoses of NMDs can assist in genetic counseling and carrier detection as well as guide therapeutic options for treatable disorders.
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Xia
authors.initials: X
authors.lastname: Tian
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Wen-Chen
authors.initials: WC
authors.lastname: Liang
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Yanming
authors.initials: Y
authors.lastname: Feng
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Victor Wei
authors.initials: VW
authors.lastname: Zhang
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Chih-Hung
authors.initials: CH
authors.lastname: Chou
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Hsien-Da
authors.initials: HD
authors.lastname: Huang
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Ching Wan
authors.initials: CW
authors.lastname: Lam
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Ya-Yun
authors.initials: YY
authors.lastname: Hsu
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Thy-Sheng
authors.initials: TS
authors.lastname: Lin
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Wan-Tzu
authors.initials: WT
authors.lastname: Chen
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Lee-Jun
authors.initials: LJ
authors.lastname: Wong
authors.affiliation: Baylor Miraca Genetics Laboratories (X.T., Y.F., J.W., V.W.Z., L.-J.W.), Houston, TX; Department of Pediatrics (W.-C.L., Y.-J.J.), Department of Laboratory Medicine (Y.-J.J.), and Department of Pathology (W.-T.C.), Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Graduate Institute of Medicine (Y.-J.J.), College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Molecular and Human Genetics (J.W., V.W.Z., L.-J.W.), Baylor College of Medicine, Houston, TX; Institute of Bioinformatics and Systems Biology (C.-H.C., H.-D.H.), and Department of Biological Science and Technology (H.-D.H., Y.-J.J.), National Chiao Tung University, Hsinchu, Taiwan; Department of Pathology (C.W.L.), The University of Hong Kong, Pokfulam, Hong Kong; and Department of Neurology (T.-S.L.), National Cheng Kung University Medical College and Hospital, Tainan, Taiwan.
authors.forename: Yuh-Jyh
authors.initials: YJ
authors.lastname: Jong