Expanding genotype/phenotype of neuromuscular diseases by comprehensive target capture/NGS

Xia Tian, Wen Chen Liang, Yanming Feng, Jing Wang, Victor Wei Zhang, Chih Hung Chou, Hsien Da Huang, Ching Wan Lam, Ya Yun Hsu, Thy-Sheng Lin, Wan Tzu Chen, Lee Jun Wong, Yuh Jyh Jong

Research output: Contribution to journalArticle

25 Citations (Scopus)

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.

Original languageEnglish
Article numbere14
JournalNeurology: Genetics
Volume1
Issue number2
DOIs
Publication statusPublished - 2015 Aug 1

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Neuromuscular Diseases
Genotype
Phenotype
High-Throughput Nucleotide Sequencing
Genes
Mutation
Heterozygote Detection
Muscles
Neuromuscular Junction
Genetic Counseling
Genetic Association Studies
Motor Neurons
Uncertainty
Exons
Nucleotides

All Science Journal Classification (ASJC) codes

  • Clinical Neurology
  • Genetics(clinical)

Cite this

Tian, X., Liang, W. C., Feng, Y., Wang, J., Zhang, V. W., Chou, C. H., ... Jong, Y. J. (2015). Expanding genotype/phenotype of neuromuscular diseases by comprehensive target capture/NGS. Neurology: Genetics, 1(2), [e14]. https://doi.org/10.1212/NXG.0000000000000015
Tian, Xia ; Liang, Wen Chen ; Feng, Yanming ; Wang, Jing ; Zhang, Victor Wei ; Chou, Chih Hung ; Huang, Hsien Da ; Lam, Ching Wan ; Hsu, Ya Yun ; Lin, Thy-Sheng ; Chen, Wan Tzu ; Wong, Lee Jun ; Jong, Yuh Jyh. / Expanding genotype/phenotype of neuromuscular diseases by comprehensive target capture/NGS. In: Neurology: Genetics. 2015 ; Vol. 1, No. 2.
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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.",
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Tian, X, Liang, WC, Feng, Y, Wang, J, Zhang, VW, Chou, CH, Huang, HD, Lam, CW, Hsu, YY, Lin, T-S, Chen, WT, Wong, LJ & Jong, YJ 2015, 'Expanding genotype/phenotype of neuromuscular diseases by comprehensive target capture/NGS', Neurology: Genetics, vol. 1, no. 2, e14. https://doi.org/10.1212/NXG.0000000000000015

Expanding genotype/phenotype of neuromuscular diseases by comprehensive target capture/NGS. / Tian, Xia; Liang, Wen Chen; Feng, Yanming; Wang, Jing; Zhang, Victor Wei; Chou, Chih Hung; Huang, Hsien Da; Lam, Ching Wan; Hsu, Ya Yun; Lin, Thy-Sheng; Chen, Wan Tzu; Wong, Lee Jun; Jong, Yuh Jyh.

In: Neurology: Genetics, Vol. 1, No. 2, e14, 01.08.2015.

Research output: Contribution to journalArticle

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AU - Tian, Xia

AU - Liang, Wen Chen

AU - Feng, Yanming

AU - Wang, Jing

AU - Zhang, Victor Wei

AU - Chou, Chih Hung

AU - Huang, Hsien Da

AU - Lam, Ching Wan

AU - Hsu, Ya Yun

AU - Lin, Thy-Sheng

AU - Chen, Wan Tzu

AU - Wong, Lee Jun

AU - Jong, Yuh Jyh

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N2 - 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.

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