RT Journal Article
SR Electronic
T1 Improving genetic diagnosis in Mendelian disease with transcriptome sequencing
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 074153
DO 10.1101/074153
A1 Beryl B Cummings
A1 Jamie L Marshall
A1 Taru Tukiainen
A1 Monkol Lek
A1 Sandra Donkervoort
A1 Reghan A. Foley
A1 Veronique Bolduc
A1 Leigh Waddell
A1 Sarah Sandaradura
A1 Gina O'Grady
A1 Elicia Estrella
A1 Hemakumar M Reddy
A1 Fengmei Zhao
A1 Ben Weisburd
A1 Konrad J Karczewski
A1 Anne O’Donnell-Luria
A1 Daniel Birnbaum
A1 Anna Sarkozy
A1 Ying Hu
A1 Hernan Gonorazky
A1 Kristl Claeys
A1 Himanshu Joshi
A1 Adam Bournazos
A1 Emily Oates
A1 Roula Ghaoui
A1 Mark Davis
A1 Nigel Laing
A1 Ana Topf
A1 GTEx Consortium
A1 Peter Kang
A1 Alan Beggs
A1 Kathryn N North
A1 Volker Straub
A1 James Dowling
A1 Francesco Muntoni
A1 Nigel F Clarke
A1 Sandra T Cooper
A1 Carsten G Bonnemann
A1 Daniel G MacArthur
YR 2016
UL http://biorxiv.org/content/early/2016/09/09/074153.abstract
AB 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 25-50% [1–4]. Here, we explore the utility of transcriptome sequencing (RNA-seq) as a complementary diagnostic tool in a cohort of 50 patients with genetically undiagnosed rare neuromuscular 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 over 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 collagen VI dystrophy in whom prior genetic analysis is negative. Overall, this study represents the largest systematic application of transcriptome sequencing to rare disease diagnosis to date and highlights its utility for the detection and interpretation of variants missed by current standard diagnostic approaches.