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A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

Authors :
Jan Hellemans
Hans Binder
Jean Thierry-Mieg
Joshua Xu
Djork-Arné Clevert
Peter Sykacek
Matthias Fischer
Youping Deng
Samir Lababidi
Ryan Peters
Hanlin Gao
Craig A. Praul
Meihua Gong
Jo Vandesompele
Haiqing Li
Wei Wang
Joaquín Dopazo
Shawn Levy
Yang Liao
John Zhang
Lee Thomas Szkotnicki
Paul Zumbo
Huixiao Hong
Weida Tong
Quan Zhen Li
E. Aubrey Thompson
Jennifer G. Catalano
Danielle Thierry-Mieg
Binsheng Gong
Wenwei Zhang
Wendell D. Jones
Min Jian
Dalila B. Megherbi
Lucille Rainbow
Robert Setterquist
Peng Li
Hong Fang
Javier Pérez-Florido
Xin Lu
Chen Zhao
Stephen J. Walker
Tao Qing
Marco Chierici
Yiming Zhou
Joseph Meehan
Christopher E. Mason
Eric D. Wieben
Mehdi Pirooznia
Liqing Wan
Bimeng Tu
Stan Letovsky
James C. Fuscoe
Sepp Hochreiter
Yoichi Gondo
Alicia Vela-Boza
Bridgett Green
Li Li
Zirui Dong
Weimin Cai
Geng Chen
Pedro Furió-Tarí
Andreas Scherer
Zhenqiang Su
Scott Schwartz
Charles Wang
Frank Staedtler
Jian Wang
Wenzhong Xiao
Yong Yang
Murray H. Brilliant
Wei Shi
Scott S. Auerbach
Matthew Tinning
Yongxiang Fang
Tingting Du
Meiwen Jia
Jiekun Xuan
Shiyong Li
Yan Li
Ying Yu
Adnan Derti
Ruchir R. Shah
Nadereh Jafari
Nancy Stralis-Pavese
Edward J. Oakeley
Jinhui Wang
Pierre R. Bushel
Jun Wang
Simon Lin
Joost H.M. van Delft
Francisco Javier López
Weigong Ge
Huan Gao
James C. Willey
Roger Perkins
Xin Xing Tan
Viswanath Devanarayan
Laure Sambourg
Zhiyu Peng
Po Yen Wu
Jianying Li
Philippe Rocca-Serra
Javier Santoyo-Lopez
Paweł P. Łabaj
David P. Kreil
Elia Stupka
John H. Phan
Heng Luo
Gary P. Schroth
Roderick V. Jensen
Thomas M. Blomquist
Russell D. Wolfinger
John F. Thompson
Wenqian Zhang
Nan Mei
Suzanne Kay
May D. Wang
Tzu Ming Chu
Jie Shen
Jiri Zavadil
Weihong Xu
Wenjun Bao
Akhilesh Pandey
Rong Chen
Leming Shi
Yutaka Suzuki
Todd M. Smith
Chao Guo
Zhuolin Gong
Feng Qian
Mario Fasold
Lei Guo
Ching-Wei Chang
Reagan Kelly
Ana Conesa
Yate Ching Yuan
Cesare Furlanello
Elisa Venturini
Zhan Ye
Yuanting Zheng
Jos C. S. Kleinjans
James Hadfield
Susanna-Assunta Sansone
Gordon K. Smyth
Li Wu Guo
Stan Gaj
Oliver Stegle
Yanyan Zhang
Tao Chen
Ye Yin
Anita Fernandez
Tieliu Shi
Charles D. Johnson
Baitang Ning
Fei Lu
Florian Caimet
Bing Mu
Jorge Gandara
Ke Zhang
Sheng Li
Xiwen Ma
Toxicogenomics
RS: GROW - Oncology
RS: GROW - R1 - Prevention
Source :
Nature biotechnology, Nature Biotechnology, 32(9), 903-914. Nature Publishing Group
Publication Year :
2014

Abstract

We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the US Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for junction discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific-filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed for all examined platforms, including qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings.

Details

Language :
English
ISSN :
10870156
Volume :
32
Issue :
9
Database :
OpenAIRE
Journal :
Nature Biotechnology
Accession number :
edsair.doi.dedup.....f574fbd57cb9cc567146ad9815046e12
Full Text :
https://doi.org/10.1038/nbt.2957