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Detection of aberrant gene expression events in RNA sequencing data

Abstract

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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Fig. 1: Workflow overview.
Fig. 2: The aberrant expression module.
Fig. 3: The aberrant splicing module.
Fig. 4: MAE module.
Fig. 5: Downstream analysis of outlier results.

Data availability

A subset of the Geuvadis dataset15 comprising 100 samples (Supplementary Data 1) was used to test and demonstrate the workflow. The original dataset is accessible without restriction under https://www.internationalgenome.org/data-portal/data-collection/geuvadis. The analyses performed in the ‘Dataset design’ section used the GTEx and Kremer et al.9 datasets. The GTEx dataset was downloaded from the GTEx Portal on 12 June 2017, under the dbGaP accession number phs00424.v6.p1. The count matrices from the Kremer et al. dataset are available on Zenodo (https://doi.org/10.5281/zenodo.3887451).

Code availability

DROP, including a small demo dataset of 10 samples and chromosome 21 only, is publicly available at https://github.com/gagneurlab/drop under MIT license. The current version is 0.9.2, which is fixed with https://doi.org/10.5281/zenodo.4106177. All the plots, results, and analyses of the test dataset can be found at https://www.cmm.in.tum.de/public/paper/drop_analysis/webDir/html/drop_analysis_index.html.

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Acknowledgements

The authors thank all the users who helped with their feedback during the revision, especially D. R. Murdock. We also thank C. Andrade for helping with the DROP logo, as well as the members of the Gagneur lab for input. The Bavaria California Technology Center supported C.M. through a fellowship. The German Bundesministerium für Bildung und Forschung (BMBF) supported the study through the e:Med Networking fonds AbCD-Net (FKZ 01ZX1706A to V.A.Y., C.M., and J.G.), the German Network for Mitochondrial Disorders (mitoNET; 01GM1113C to H.P.), the E-Rare project GENOMIT (01GM1920A to M.G. and H.P.), the Medical Informatics Initiative CORD-MI (Collaboration on Rare Diseases) to V.A.Y., and the ERA PerMed project PerMiM (01KU2016A to H.P. and J.G.). The Genotype-Tissue Expression (GTEx) project was supported by the Common Fund of the Office of the Director of the National Institutes of Health, and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS.

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Authors

Contributions

V.A.Y., C.M., M.F.M., and J.G. participated to the design of the workflow. V.A.Y., C.M., M.F.M., D.K-A., I.F.S., and P.F.G. contributed to the computational workflow. L.F. implemented the candidate prioritization workflow. L.W. designed and implemented wBuild. V.A.Y. and J.G. wrote the manuscript with the help of L.F, D.K-A., M.G., I.F.S., and H.P. C.M., H.P., and J.G. supervised the research. All authors revised the manuscript.

Corresponding author

Correspondence to Julien Gagneur.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Protocols thanks Anna Esteve-Codina and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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Key references using this protocol

Kremer, L. et al. Nat. Commun. 8, 15824 (2017): https://doi.org/10.1038/ncomms15824

Murdock, D. R. et al. J. Clin. Invest. (2020): https://doi.org/10.1172/JCI141500

Key data used in this protocol

Kremer, L. et al. Nat. Commun. 8, 15824 (2017): https://doi.org/10.1038/ncomms15824

GTEx Consortium. Nature 550, 7675 (2017): https://doi.org/10.1038/nature24277

Lappalainen, T. et al. Nature 501, 7468 (2013): https://doi.org/10.1038/nature12531

Supplementary information

Supplementary Information

Supplementary Figs. 1–8 and Supplementary Methods.

Reporting Summary

Supplementary Data 1

Sample annotation of the test dataset.

Supplementary Data 2

Configuration file for the test dataset.

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Yépez, V.A., Mertes, C., Müller, M.F. et al. Detection of aberrant gene expression events in RNA sequencing data. Nat Protoc 16, 1276–1296 (2021). https://doi.org/10.1038/s41596-020-00462-5

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