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Velluva, A.* ; Radtke, M.* ; Horn, S.* ; Popp, B.* ; Platzer, K.* ; Gjermeni, E.* ; Lin, C.C.* ; Lemke, J.R.* ; Garten, A.* ; Schöneberg, T.* ; Blüher, M. ; Abou Jamra, R.* ; Le Duc, D.

Phenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies.

BMC Genomics 22:802 (2021)
Verlagsversion Forschungsdaten DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
BACKGROUND: RNA-seq emerges as a valuable method for clinical genetics. The transcriptome is "dynamic" and tissue-specific, but typically the probed tissues to analyze (TA) are different from the tissue of interest (TI) based on pathophysiology. RESULTS: We developed Phenotype-Tissue Expression and Exploration (PTEE), a tool to facilitate the decision about the most suitable TA for RNA-seq. We integrated phenotype-annotated genes, used 54 tissues from GTEx to perform correlation analyses and identify expressed genes and transcripts between TAs and TIs. We identified skeletal muscle as the most appropriate TA to inquire for cardiac arrhythmia genes and skin as a good proxy to study neurodevelopmental disorders. We also explored RNA-seq limitations and show that on-off switching of gene expression during ontogenesis or circadian rhythm can cause blind spots for RNA-seq-based analyses. CONCLUSIONS: PTEE aids the identification of tissues suitable for RNA-seq for a given pathology to increase the success rate of diagnosis and gene discovery. PTEE is freely available at https://bioinf.eva.mpg.de/PTEE/.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Diagnosis; Adult
ISSN (print) / ISBN 1471-2164
e-ISSN 1471-2164
Zeitschrift BMC Genomics
Quellenangaben Band: 22, Heft: 1, Seiten: , Artikelnummer: 802 Supplement: ,
Verlag BioMed Central
Verlagsort Campus, 4 Crinan St, London N1 9xw, England
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Helmholtz Institute for Metabolism, Obesity and Vascular Research (HI-MAG)
Förderungen Projekt DEAL
Else-Kroner Fresenius Foundation
Deutsche Forschungsgemeinschaft (DFG, German Research foundation)
Clinician Scientist Programm, Medizinische Fakultat der Universitat Leipzig