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Improving genetic diagnosis in Mendelian disease with transcriptome sequencing.

Publication ,  Journal Article
Cummings, BB; Marshall, JL; Tukiainen, T; Lek, M; Donkervoort, S; Foley, AR; Bolduc, V; Waddell, LB; Sandaradura, SA; O'Grady, GL; Estrella, E ...
Published in: Science translational medicine
April 2017

Exome and whole-genome sequencing are becoming increasingly routine approaches in Mendelian disease diagnosis. Despite their success, the current diagnostic rate for genomic analyses across a variety of rare diseases is approximately 25 to 50%. We explore the utility of transcriptome sequencing [RNA sequencing (RNA-seq)] as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare muscle disorders. We describe an integrated approach to analyze patient muscle RNA-seq, leveraging an analysis framework focused on the detection of transcript-level changes that are unique to the patient compared to more than 180 control skeletal muscle samples. We demonstrate the power of RNA-seq to validate candidate splice-disrupting mutations and to identify splice-altering variants in both exonic and deep intronic regions, yielding an overall diagnosis rate of 35%. We also report the discovery of a highly recurrent de novo intronic mutation in COL6A1 that results in a dominantly acting splice-gain event, disrupting the critical glycine repeat motif of the triple helical domain. We identify this pathogenic variant in a total of 27 genetically unsolved patients in an external collagen VI-like dystrophy cohort, thus explaining approximately 25% of patients clinically suggestive of having collagen VI dystrophy in whom prior genetic analysis is negative. Overall, this study represents a large systematic application of transcriptome sequencing to rare disease diagnosis and highlights its utility for the detection and interpretation of variants missed by current standard diagnostic approaches.

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Published In

Science translational medicine

DOI

EISSN

1946-6242

ISSN

1946-6234

Publication Date

April 2017

Volume

9

Issue

386

Start / End Page

eaal5209

Related Subject Headings

  • Transcriptome
  • Mutation
  • Muscular Diseases
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Collagen Type VI
  • 4003 Biomedical engineering
  • 3206 Medical biotechnology
  • 11 Medical and Health Sciences
  • 06 Biological Sciences
 

Citation

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Cummings, B. B., Marshall, J. L., Tukiainen, T., Lek, M., Donkervoort, S., Foley, A. R., … MacArthur, D. G. (2017). Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Science Translational Medicine, 9(386), eaal5209. https://doi.org/10.1126/scitranslmed.aal5209
Cummings, Beryl B., Jamie L. Marshall, Taru Tukiainen, Monkol Lek, Sandra Donkervoort, A Reghan Foley, Veronique Bolduc, et al. “Improving genetic diagnosis in Mendelian disease with transcriptome sequencing.Science Translational Medicine 9, no. 386 (April 2017): eaal5209. https://doi.org/10.1126/scitranslmed.aal5209.
Cummings BB, Marshall JL, Tukiainen T, Lek M, Donkervoort S, Foley AR, et al. Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Science translational medicine. 2017 Apr;9(386):eaal5209.
Cummings, Beryl B., et al. “Improving genetic diagnosis in Mendelian disease with transcriptome sequencing.Science Translational Medicine, vol. 9, no. 386, Apr. 2017, p. eaal5209. Epmc, doi:10.1126/scitranslmed.aal5209.
Cummings BB, Marshall JL, Tukiainen T, Lek M, Donkervoort S, Foley AR, Bolduc V, Waddell LB, Sandaradura SA, O’Grady GL, Estrella E, Reddy HM, Zhao F, Weisburd B, Karczewski KJ, O’Donnell-Luria AH, Birnbaum D, Sarkozy A, Hu Y, Gonorazky H, Claeys K, Joshi H, Bournazos A, Oates EC, Ghaoui R, Davis MR, Laing NG, Topf A, Genotype-Tissue Expression Consortium, Kang PB, Beggs AH, North KN, Straub V, Dowling JJ, Muntoni F, Clarke NF, Cooper ST, Bönnemann CG, MacArthur DG. Improving genetic diagnosis in Mendelian disease with transcriptome sequencing. Science translational medicine. 2017 Apr;9(386):eaal5209.

Published In

Science translational medicine

DOI

EISSN

1946-6242

ISSN

1946-6234

Publication Date

April 2017

Volume

9

Issue

386

Start / End Page

eaal5209

Related Subject Headings

  • Transcriptome
  • Mutation
  • Muscular Diseases
  • Humans
  • High-Throughput Nucleotide Sequencing
  • Collagen Type VI
  • 4003 Biomedical engineering
  • 3206 Medical biotechnology
  • 11 Medical and Health Sciences
  • 06 Biological Sciences