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Yépez, V.A.* ; Mertes, C.* ; Müller, M.F.* ; Wachutka, L.* ; Frésard, L.* ; Gusic, M. ; Scheller, I.F.* ; Goldberg, P.F.* ; Prokisch, H. ; Gagneur, J.

Detection of aberrant gene expression events in RNA sequencing data.

Nat. Protoc. 16, 1276–1296 (2021)
Postprint DOI PMC
Open Access Green
RNA sequencing (RNA-seq) has emerged as a powerful approach to discover disease-causing gene regulatory defects in individuals affected by genetically undiagnosed rare disorders. Pioneering studies have shown that RNA-seq could increase the diagnosis rates over DNA sequencing alone by 8-36%, depending on the disease entity and tissue probed. To accelerate adoption of RNA-seq by human genetics centers, detailed analysis protocols are now needed. We present a step-by-step protocol that details how to robustly detect aberrant expression levels, aberrant splicing and mono-allelic expression in RNA-seq data using dedicated statistical methods. We describe how to generate and assess quality control plots and interpret the analysis results. The protocol is based on the detection of RNA outliers pipeline (DROP), a modular computational workflow that integrates all the analysis steps, can leverage parallel computing infrastructures and generates browsable web page reports.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Messenger-rna; Diagnosis; Transcriptome; Multiple; Disease; Format
ISSN (print) / ISBN 1754-2189
e-ISSN 1750-2799
Journal Nature Protocols
Quellenangaben Volume: 16, Issue: , Pages: 1276–1296 Article Number: , Supplement: ,
Publisher Nature Publishing Group
Publishing Place Heidelberger Platz 3, Berlin, 14197, Germany
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)
Institute of Neurogenomics (ING)
Grants NHGRI
German Bundesministerium fur Bildung und Forschung (BMBF) through German Network for Mitochondrial Disorders (mitoNET)
NINDS
NIMH
NIDA
NHLBI
NCI
Common Fund of the Office of the Director of the National Institutes of Health
German Bundesministerium fur Bildung und Forschung (BMBF) through ERA PerMed project PerMiM
German Bundesministerium fur Bildung und Forschung (BMBF) through Medical Informatics Initiative CORD-MI (Collaboration on Rare Diseases)
German Bundesministerium fur Bildung und Forschung (BMBF) through the e:Med Networking fonds AbCD-Net
Bavaria California Technology Center
German Bundesministerium fur Bildung und Forschung (BMBF) through E-Rare project GENOMIT