Improving genetic diagnosis in Mendelian disease with transcriptome sequencing.

TitleImproving genetic diagnosis in Mendelian disease with transcriptome sequencing.
Publication TypeJournal Article
Year of Publication2017
AuthorsCummings, BB, Marshall, JL, Tukiainen, T, Lek, M, Donkervoort, S, A Foley, R, 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, Kang, PB, Beggs, AH, North, KN, Straub, V, Dowling, JJ, Muntoni, F, Clarke, NF, Cooper, ST, Bönnemann, CG, MacArthur, DG
Corporate AuthorsGenotype-Tissue Expression Consortium
JournalSci Transl Med
Date Published2017 04 19
KeywordsCollagen Type VI, High-Throughput Nucleotide Sequencing, Humans, Muscular Diseases, Mutation, Transcriptome

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 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.

Alternate JournalSci Transl Med
PubMed ID28424332
PubMed Central IDPMC5548421
Grant ListUM1 HG008900 / HG / NHGRI NIH HHS / United States
R01 DA006227 / DA / NIDA NIH HHS / United States
R01 AR044345 / AR / NIAMS NIH HHS / United States
R01 HD075802 / HD / NICHD NIH HHS / United States
T32 GM096911 / GM / NIGMS NIH HHS / United States
U54 HD090255 / HD / NICHD NIH HHS / United States
/ / Wellcome Trust / United Kingdom
HHSN261200800001C / RC / CCR NIH HHS / United States
R01 GM104371 / GM / NIGMS NIH HHS / United States
F32 GM115208 / GM / NIGMS NIH HHS / United States
T32 GM007748 / GM / NIGMS NIH HHS / United States
HHSN268201000029C / HL / NHLBI NIH HHS / United States
HHSN261200800001E / CA / NCI NIH HHS / United States
L60 MD010032 / MD / NIMHD NIH HHS / United States
R01 NS080929 / NS / NINDS NIH HHS / United States