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

Abstract 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 Expressi...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Akhil Velluva, Maximillian Radtke, Susanne Horn, Bernt Popp, Konrad Platzer, Erind Gjermeni, Chen-Ching Lin, Johannes R. Lemke, Antje Garten, Torsten Schöneberg, Matthias Blüher, Rami Abou Jamra, Diana Le Duc
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/ac3037e353d248199606be6e0d9be1b9
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:ac3037e353d248199606be6e0d9be1b9
record_format	dspace
spelling	oai:doaj.org-article:ac3037e353d248199606be6e0d9be1b92021-11-14T12:26:42ZPhenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies10.1186/s12864-021-08125-91471-2164https://doaj.org/article/ac3037e353d248199606be6e0d9be1b92021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08125-9https://doaj.org/toc/1471-2164Abstract 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/Akhil VelluvaMaximillian RadtkeSusanne HornBernt PoppKonrad PlatzerErind GjermeniChen-Ching LinJohannes R. LemkeAntje GartenTorsten SchönebergMatthias BlüherRami Abou JamraDiana Le DucBMCarticleBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-9 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Biotechnology TP248.13-248.65 Genetics QH426-470 Akhil Velluva Maximillian Radtke Susanne Horn Bernt Popp Konrad Platzer Erind Gjermeni Chen-Ching Lin Johannes R. Lemke Antje Garten Torsten Schöneberg Matthias Blüher Rami Abou Jamra Diana Le Duc Phenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies
description	Abstract 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/
format	article
author	Akhil Velluva Maximillian Radtke Susanne Horn Bernt Popp Konrad Platzer Erind Gjermeni Chen-Ching Lin Johannes R. Lemke Antje Garten Torsten Schöneberg Matthias Blüher Rami Abou Jamra Diana Le Duc
author_facet	Akhil Velluva Maximillian Radtke Susanne Horn Bernt Popp Konrad Platzer Erind Gjermeni Chen-Ching Lin Johannes R. Lemke Antje Garten Torsten Schöneberg Matthias Blüher Rami Abou Jamra Diana Le Duc
author_sort	Akhil Velluva
title	Phenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies
title_short	Phenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies
title_full	Phenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies
title_fullStr	Phenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies
title_full_unstemmed	Phenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies
title_sort	phenotype-tissue expression and exploration (ptee) resource facilitates the choice of tissue for rna-seq-based clinical genetics studies
publisher	BMC
publishDate	2021
url	https://doaj.org/article/ac3037e353d248199606be6e0d9be1b9
work_keys_str_mv	AT akhilvelluva phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies AT maximillianradtke phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies AT susannehorn phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies AT berntpopp phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies AT konradplatzer phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies AT erindgjermeni phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies AT chenchinglin phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies AT johannesrlemke phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies AT antjegarten phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies AT torstenschoneberg phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies AT matthiasbluher phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies AT ramiaboujamra phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies AT dianaleduc phenotypetissueexpressionandexplorationpteeresourcefacilitatesthechoiceoftissueforrnaseqbasedclinicalgeneticsstudies
_version_	1718429249797357568

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

Ejemplares similares