Cited by 759Hereditary Neurological DisordersGenomics and Rare DiseasesMetabolism and Genetic Disorders

Whole-Genome Sequencing in a Patient with Charcot–Marie–Tooth Neuropathy

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Lupski, James R., Reid, Jeffrey G., Gonzaga-Jauregui, Claudia, Rio Deiros, David, Chen, David C.Y., Nazareth, Lynne, Bainbridge, Matthew, Dinh, Huyen +14 more·2010·New England Journal of Medicine

Abstract

BACKGROUND: Whole-genome sequencing may revolutionize medical diagnostics through rapid identification of alleles that cause disease. However, even in cases with simple patterns of inheritance and unambiguous diagnoses, the relationship between disease phenotypes and their corresponding genetic changes can be complicated. Comprehensive diagnostic assays must therefore identify all possible DNA changes in each haplotype and determine which are responsible for the underlying disorder. The high number of rare, heterogeneous mutations present in all humans and the paucity of known functional variants in more than 90% of annotated genes make this challenge particularly difficult. Thus, the identification of the molecular basis of a genetic disease by means of whole-genome sequencing has remained elusive. We therefore aimed to assess the usefulness of human whole-genome sequencing for genetic diagnosis in a patient with Charcot-Marie-Tooth disease. METHODS: We identified a family with a recessive form of Charcot-Marie-Tooth disease for which the genetic basis had not been identified. We sequenced the whole genome of the proband, identified all potential functional variants in genes likely to be related to the disease, and genotyped these variants in the affected family members. RESULTS: We identified and validated compound, heterozygous, causative alleles in SH3TC2 (the SH3 domain and tetratricopeptide repeats 2 gene), involving two mutations, in the proband and in family members affected by Charcot-Marie-Tooth disease. Separate subclinical phenotypes segregated independently with each of the two mutations; heterozygous mutations confer susceptibility to neuropathy, including the carpal tunnel syndrome. CONCLUSIONS: As shown in this study of a family with Charcot-Marie-Tooth disease, whole-genome sequencing can identify clinically relevant variants and provide diagnostic information to inform the care of patients.

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  • The most plausible explanation for incorrect detection of c.1823 G>A as a non-deleterious SNP is that the same variant is present in an ABCD1 pseudogene on chromosome 2 and was mistakenly attributed to the real ABCD1 gene.

    “Therefore, the most plausible explanation for the incorrect detection of the mutation in the former study52 is that the same variant is present in an ABCD1 pseudogene located on chromosome 2 and was by mistake attributed to the real ABCD1 gene.”

    From The genetic landscape of X-linked adrenoleukodystrophy: inheritance, mutations, modifier genes, and diagnosis (2015) · cites this paper as [52]

    The Results (Genome Variation; page unavailable) report an ABCD1 SNP in a patient without adrenoleukodystrophy and suggest that its classification as a disease mutation might be erroneous. The paper does not identify c.1823 G>A, an ABCD1 pseudogene on chromosome 2, or mistaken attribution to the real gene as the explanation. The citing authors present that explanation as their own inference. (LLM, conf=0.85)

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Authors
Lupski, J. R., Reid, J. G., Gonzaga-Jauregui, C., Rio Deiros, D., Chen, D. C. Y., Nazareth, L., Bainbridge, M., Dinh, H., Jing, C., Wheeler, D. A., McGuire, A. L., Zhang, F., Stankiewicz, P., Halperin, J. J., Yang, C., Gehman, C., Guo, D., Irikat, R. K., Tom, W., Fantin, N. J., Muzny, D. M., & Gibbs, R. A.
Affiliations
  • Baylor College of Medicine (US)
  • Icahn School of Medicine at Mount Sinai (US)
Venue
New England Journal of Medicine
Published
2010-04
Volume
362
Issue
13
Pages
1181-1191
ISSN
  • 0028-4793 (ISSN-L)
  • 1533-4406
OpenAlex
W2118246164
Cited by
759
References
40
Citations by year
2026: 4 · 2025: 11 · 2024: 14 · 2023: 10 · 2022: 12 · 2021: 27 · 2020: 20 · 2019: 25 · 2018: 19 · 2017: 23 · 2016: 41 · 2015: 52 · 2014: 76 · 2013: 82 · 2012: 132
FWCI
54.74
Type
journal article
Language
en
Open access
Locations
  • New England Journal of Medicine (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Human Genome Research Institute (U54HG003273)
  • National Institute of Neurological Disorders and Stroke (R01NS058529)
Topics
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Hereditary Neurological Disorders
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Metabolism and Genetic Disorders
Keywords
Charcot-Marie-Tooth disease, whole genome sequencing, genetic diagnosis, recessive inheritance, SH3TC2, compound heterozygosity, carpal tunnel syndrome, rare variants
MeSH terms
Adult, Aged, Aged, 80 and over, Charcot-Marie-Tooth Disease, Female, Genes, Recessive, Genotype, Humans, Male, Middle Aged, Pedigree, Phenotype, Genome, Human, Sequence Analysis, DNA, Codon, Nonsense, Mutation, Missense, Polymorphism, Single Nucleotide, Genetic Association Studies

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