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Yépez, V.A.* ; Gusic, M. ; Kopajtich, R. ; Mertes, C.* ; Smith, N.H.* ; Alston, C.L.* ; Ban, R. ; Beblo, S.* ; Berutti, R. ; Blessing, H.* ; Ciara, E.* ; Distelmaier, F.* ; Freisinger, P.* ; Häberle, J.* ; Hayflick, S.J.* ; Hempel, M.* ; Itkis, Y.S.* ; Kishita, Y.* ; Klopstock, T.* ; Krylova, T.D.* ; Lamperti, C.* ; Lenz, D.* ; Makowski, C.* ; Mosegaard, S.* ; Müller, M.F.* ; Muñoz-Pujol, G.* ; Nadel, A. ; Ohtake, A.* ; Okazaki, Y.* ; Procopio, E.* ; Schwarzmayr, T. ; Smet, J.* ; Staufner, C.* ; Stenton, S. ; Strom, T.-M. ; Terrile, C. ; Tort, F.* ; van Coster, R.* ; Vanlander, A.* ; Wagner, M. ; Xu, M. ; Fang, F.* ; Ghezzi, D.* ; Mayr, J.A.* ; Piekutowska-Abramczuk, D.* ; Ribes, A.* ; Rötig, A.* ; Taylor, R.W.* ; Wortmann, S.B.* ; Murayama, K.* ; Meitinger, T.* ; Gagneur, J. ; Prokisch, H.

Clinical implementation of RNA sequencing for Mendelian disease diagnostics.

Genome Med. 14:38 (2022)
Publ. Version/Full Text Research data DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
BACKGROUND: Lack of functional evidence hampers variant interpretation, leaving a large proportion of individuals with a suspected Mendelian disorder without genetic diagnosis after whole genome or whole exome sequencing (WES). Research studies advocate to further sequence transcriptomes to directly and systematically probe gene expression defects. However, collection of additional biopsies and establishment of lab workflows, analytical pipelines, and defined concepts in clinical interpretation of aberrant gene expression are still needed for adopting RNA sequencing (RNA-seq) in routine diagnostics. METHODS: We implemented an automated RNA-seq protocol and a computational workflow with which we analyzed skin fibroblasts of 303 individuals with a suspected mitochondrial disease that previously underwent WES. We also assessed through simulations how aberrant expression and mono-allelic expression tests depend on RNA-seq coverage. RESULTS: We detected on average 12,500 genes per sample including around 60% of all disease genes-a coverage substantially higher than with whole blood, supporting the use of skin biopsies. We prioritized genes demonstrating aberrant expression, aberrant splicing, or mono-allelic expression. The pipeline required less than 1 week from sample preparation to result reporting and provided a median of eight disease-associated genes per patient for inspection. A genetic diagnosis was established for 16% of the 205 WES-inconclusive cases. Detection of aberrant expression was a major contributor to diagnosis including instances of 50% reduction, which, together with mono-allelic expression, allowed for the diagnosis of dominant disorders caused by haploinsufficiency. Moreover, calling aberrant splicing and variants from RNA-seq data enabled detecting and validating splice-disrupting variants, of which the majority fell outside WES-covered regions. CONCLUSION: Together, these results show that streamlined experimental and computational processes can accelerate the implementation of RNA-seq in routine diagnostics.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Genetic Diagnostics ; Mendelian Diseases ; Rna-seq
ISSN (print) / ISBN 1756-994X
e-ISSN 1756-994X
Journal Genome Medicine
Quellenangaben Volume: 14, Issue: 1, Pages: , Article Number: 38 Supplement: ,
Publisher BioMed Central
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Neurogenomics (ING)
Institute of Computational Biology (ICB)
Grants Wellcome Trust Centre for Mitochondrial Research
Instituto de Salud Carlos III
Agency for Medical Research and Development (JP)
National Institute for Health Research
Bundesministerium für Bildung und Forschung