Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors

Abstract The availability of fresh frozen (FF) tissue is a barrier for implementing RNA sequencing (RNA-seq) in the clinic. The majority of clinical samples are stored as formalin-fixed, paraffin-embedded (FFPE) tissues. Exome capture platforms have been developed for RNA-seq from FFPE samples. Howe...

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Autores principales:	Kyrillus S. Shohdy, Rohan Bareja, Michael Sigouros, David C. Wilkes, Princesca Dorsaint, Jyothi Manohar, Daniel Bockelman, Jenny Z. Xiang, Rob Kim, Kentaro Ohara, Kenneth Eng, Juan Miguel Mosquera, Olivier Elemento, Andrea Sboner, Alicia Alonso, Bishoy M. Faltas
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Genetics QH426-470
Acceso en línea:	https://doaj.org/article/be290d96afc142fb9fcbd3a2e94604c7
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spelling	oai:doaj.org-article:be290d96afc142fb9fcbd3a2e94604c72021-12-02T18:50:45ZFunctional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors10.1038/s41525-021-00231-72056-7944https://doaj.org/article/be290d96afc142fb9fcbd3a2e94604c72021-08-01T00:00:00Zhttps://doi.org/10.1038/s41525-021-00231-7https://doaj.org/toc/2056-7944Abstract The availability of fresh frozen (FF) tissue is a barrier for implementing RNA sequencing (RNA-seq) in the clinic. The majority of clinical samples are stored as formalin-fixed, paraffin-embedded (FFPE) tissues. Exome capture platforms have been developed for RNA-seq from FFPE samples. However, these methods have not been systematically compared. We performed transcriptomic analysis of 32 FFPE tumor samples from 11 patients using three exome capture-based methods: Agilent SureSelect V6, TWIST NGS Exome, and IDT XGen Exome Research Panel. We compared these methods to the TruSeq RNA-seq of fresh frozen (FF-TruSeq) tumor samples from the same patients. We assessed the recovery of clinically relevant biological features. The Spearman’s correlation coefficients between the global expression profiles of the three capture-based methods from FFPE and matched FF-TruSeq were high (rho = 0.72–0.9, p < 0.05). A significant correlation between the expression of key immune genes between individual capture-based methods and FF-TruSeq (rho = 0.76-0.88, p < 0.05) was observed. All exome capture-based methods reliably detected outlier expression of actionable gene transcripts, including ERBB2, MET, NTRK1, and PPARG. In urothelial cancer samples, the Agilent assay was associated with the highest molecular subtype concordance with FF-TruSeq (Cohen’s k = 0.7, p < 0.01). The Agilent and IDT assays detected all the clinically relevant fusions that were initially identified in FF-TruSeq. All FFPE exome capture-based methods had comparable performance and concordance with FF-TruSeq. Our findings will enable the implementation of RNA-seq in the clinic to guide precision oncology approaches.Kyrillus S. ShohdyRohan BarejaMichael SigourosDavid C. WilkesPrincesca DorsaintJyothi ManoharDaniel BockelmanJenny Z. XiangRob KimKentaro OharaKenneth EngJuan Miguel MosqueraOlivier ElementoAndrea SbonerAlicia AlonsoBishoy M. FaltasNature PortfolioarticleMedicineRGeneticsQH426-470ENnpj Genomic Medicine, Vol 6, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Genetics QH426-470
spellingShingle	Medicine R Genetics QH426-470 Kyrillus S. Shohdy Rohan Bareja Michael Sigouros David C. Wilkes Princesca Dorsaint Jyothi Manohar Daniel Bockelman Jenny Z. Xiang Rob Kim Kentaro Ohara Kenneth Eng Juan Miguel Mosquera Olivier Elemento Andrea Sboner Alicia Alonso Bishoy M. Faltas Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors
description	Abstract The availability of fresh frozen (FF) tissue is a barrier for implementing RNA sequencing (RNA-seq) in the clinic. The majority of clinical samples are stored as formalin-fixed, paraffin-embedded (FFPE) tissues. Exome capture platforms have been developed for RNA-seq from FFPE samples. However, these methods have not been systematically compared. We performed transcriptomic analysis of 32 FFPE tumor samples from 11 patients using three exome capture-based methods: Agilent SureSelect V6, TWIST NGS Exome, and IDT XGen Exome Research Panel. We compared these methods to the TruSeq RNA-seq of fresh frozen (FF-TruSeq) tumor samples from the same patients. We assessed the recovery of clinically relevant biological features. The Spearman’s correlation coefficients between the global expression profiles of the three capture-based methods from FFPE and matched FF-TruSeq were high (rho = 0.72–0.9, p < 0.05). A significant correlation between the expression of key immune genes between individual capture-based methods and FF-TruSeq (rho = 0.76-0.88, p < 0.05) was observed. All exome capture-based methods reliably detected outlier expression of actionable gene transcripts, including ERBB2, MET, NTRK1, and PPARG. In urothelial cancer samples, the Agilent assay was associated with the highest molecular subtype concordance with FF-TruSeq (Cohen’s k = 0.7, p < 0.01). The Agilent and IDT assays detected all the clinically relevant fusions that were initially identified in FF-TruSeq. All FFPE exome capture-based methods had comparable performance and concordance with FF-TruSeq. Our findings will enable the implementation of RNA-seq in the clinic to guide precision oncology approaches.
format	article
author	Kyrillus S. Shohdy Rohan Bareja Michael Sigouros David C. Wilkes Princesca Dorsaint Jyothi Manohar Daniel Bockelman Jenny Z. Xiang Rob Kim Kentaro Ohara Kenneth Eng Juan Miguel Mosquera Olivier Elemento Andrea Sboner Alicia Alonso Bishoy M. Faltas
author_facet	Kyrillus S. Shohdy Rohan Bareja Michael Sigouros David C. Wilkes Princesca Dorsaint Jyothi Manohar Daniel Bockelman Jenny Z. Xiang Rob Kim Kentaro Ohara Kenneth Eng Juan Miguel Mosquera Olivier Elemento Andrea Sboner Alicia Alonso Bishoy M. Faltas
author_sort	Kyrillus S. Shohdy
title	Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors
title_short	Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors
title_full	Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors
title_fullStr	Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors
title_full_unstemmed	Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors
title_sort	functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/be290d96afc142fb9fcbd3a2e94604c7
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Functional comparison of exome capture-based methods for transcriptomic profiling of formalin-fixed paraffin-embedded tumors

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