@article {Cummings074153, author = {Beryl B Cummings and Jamie L Marshall and Taru Tukiainen and Monkol Lek and Sandra Donkervoort and Reghan A. Foley and Veronique Bolduc and Leigh Waddell and Sarah Sandaradura and Gina O{\textquoteright}Grady and Elicia Estrella and Hemakumar M Reddy and Fengmei Zhao and Ben Weisburd and Konrad J Karczewski and Anne O{\textquoteright}Donnell-Luria and Daniel Birnbaum and Anna Sarkozy and Ying Hu and Hernan Gonorazky and Kristl Claeys and Himanshu Joshi and Adam Bournazos and Emily Oates and Roula Ghaoui and Mark Davis and Nigel Laing and Ana Topf and GTEx Consortium and Peter Kang and Alan Beggs and Kathryn N North and Volker Straub and James Dowling and Francesco Muntoni and Nigel F Clarke and Sandra T Cooper and Carsten G Bonnemann and Daniel G MacArthur}, title = {Improving genetic diagnosis in Mendelian disease with transcriptome sequencing}, elocation-id = {074153}, year = {2016}, doi = {10.1101/074153}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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{\textendash}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.}, URL = {https://www.biorxiv.org/content/early/2016/09/09/074153}, eprint = {https://www.biorxiv.org/content/early/2016/09/09/074153.full.pdf}, journal = {bioRxiv} }