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

Zhenqiang Su, Paweł P. Łabaj, Sheng Li, Jean Thierry-Mieg, Danielle Thierry-Mieg, Wei Shi, Charles Wang, Gary P. Schroth, Robert A. Setterquist, John F. Thompson, Wendell D. Jones, Wenzhong Xiao, Weihong Xu, Roderick V. Jensen, Reagan Kelly, Joshua Xu, Ana Conesa, Cesare Furlanello, Hanlin Gao, Huixiao Hong & 142 others Nadereh Jafari, Stan Letovsky, Yang Liao, Fei Lu, Edward J. Oakeley, Zhiyu Peng, Craig A. Praul, Javier Santoyo-Lopez, Andreas Scherer, Tieliu Shi, Gordon K. Smyth, Frank Staedtler, Peter Sykacek, Xin Xing Tan, E. Aubrey Thompson, Jo Vandesompele, May D. Wang, Jian Wang, Russell D. Wolfinger, Jiri Zavadil, Scott S. Auerbach, Wenjun Bao, Hans Binder, Thomas Blomquist, Murray H. Brilliant, Pierre R. Bushel, Weimin Cai, Jennifer G. Catalano, Ching Wei Chang, Tao Chen, Geng Chen, Rong Chen, Marco Chierici, Tzu Ming Chu, Djork Arné Clevert, Youping Deng, Adnan Derti, Viswanath Devanarayan, Zirui Dong, Joaquin Dopazo, Tingting Du, Hong Fang, Yongxiang Fang, Mario Fasold, Anita Fernandez, Matthias Fischer, Pedro Furió-Tari, James C. Fuscoe, Florian Caimet, Stan Gaj, Jorge Gandara, Huan Gao, Weigong Ge, Yoichi Gondo, Binsheng Gong, Meihua Gong, Zhuolin Gong, Bridgett Green, Chao Guo, Lei Guo, Li Wu Guo, James Hadfield, Jan Hellemans, Sepp Hochreiter, Meiwen Jia, Min Jian, Charles D. Johnson, Suzanne Kay, Jos Kleinjans, Samir Lababidi, Shawn Levy, Quan Zhen Li, Li Li, Li Li, Peng Li, Yan Li, Haiqing Li, Jianying Li, Shiyong Li, Simon M. Lin, Francisco J. López, Xin Lu, Heng Luo, Xiwen Ma, Joseph Meehan, Dalila B. Megherbi, Nan Mei, Bing Mu, Baitang Ning, Akhilesh Pandey, Javier Pérez-Florido, Roger G. Perkins, Ryan Peters, John H. Phan, Mehdi Pirooznia, Feng Qian, Tao Qing, Lucille Rainbow, Philippe Rocca-Serra, Laure Sambourg, Susanna Assunta Sansone, Scott Schwartz, Ruchir Shah, Jie Shen, Todd M. Smith, Oliver Stegle, Nancy Stralis-Pavese, Elia Stupka, Yutaka Suzuki, Lee T. Szkotnicki, Matthew Tinning, Bimeng Tu, Joost Van Delft, Alicia Vela-Boza, Elisa Venturini, Stephen J. Walker, Liqing Wan, Wei Wang, Jinhui Wang, Jun Wang, Eric D. Wieben, James C. Willey, Po Yen Wu, Jiekun Xuan, Yong Yang, Zhan Ye, Ye Yin, Ying Yu, Yate Ching Yuan, John Zhang, Ke K. Zhang, Wenqian Zhang, Wenwei Zhang, Yanyan Zhang, Chen Zhao, Yuanting Zheng, Yiming Zhou, Paul Zumbo, Weida Tong, David P. Kreil, Christopher E. Mason, Leming Shi

Research output: Contribution to journalArticle

376 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)903-914
Number of pages12
JournalNature Biotechnology
Volume32
Issue number9
DOIs
StatePublished - Sep 1 2014

Fingerprint

RNA Sequence Analysis
RNA
Quality Control
Quality control
Polymerase Chain Reaction
Exons
Microarrays
United States Food and Drug Administration
Technology
Pipelines
Genes

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Biotechnology
  • Molecular Medicine
  • Bioengineering
  • Biomedical Engineering

Cite this

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

In: Nature Biotechnology, Vol. 32, No. 9, 01.09.2014, p. 903-914.

Research output: Contribution to journalArticle

Su, Z, Łabaj, PP, Li, S, Thierry-Mieg, J, Thierry-Mieg, D, Shi, W, Wang, C, Schroth, GP, Setterquist, RA, Thompson, JF, Jones, WD, Xiao, W, Xu, W, Jensen, RV, Kelly, R, Xu, J, Conesa, A, Furlanello, C, Gao, H, Hong, H, Jafari, N, Letovsky, S, Liao, Y, Lu, F, Oakeley, EJ, Peng, Z, Praul, CA, Santoyo-Lopez, J, Scherer, A, Shi, T, Smyth, GK, Staedtler, F, Sykacek, P, Tan, XX, Thompson, EA, Vandesompele, J, Wang, MD, Wang, J, Wolfinger, RD, Zavadil, J, Auerbach, SS, Bao, W, Binder, H, Blomquist, T, Brilliant, MH, Bushel, PR, Cai, W, Catalano, JG, Chang, CW, Chen, T, Chen, G, Chen, R, Chierici, M, Chu, TM, Clevert, DA, Deng, Y, Derti, A, Devanarayan, V, Dong, Z, Dopazo, J, Du, T, Fang, H, Fang, Y, Fasold, M, Fernandez, A, Fischer, M, Furió-Tari, P, Fuscoe, JC, Caimet, F, Gaj, S, Gandara, J, Gao, H, Ge, W, Gondo, Y, Gong, B, Gong, M, Gong, Z, Green, B, Guo, C, Guo, L, Guo, LW, Hadfield, J, Hellemans, J, Hochreiter, S, Jia, M, Jian, M, Johnson, CD, Kay, S, Kleinjans, J, Lababidi, S, Levy, S, Li, QZ, Li, L, Li, L, Li, P, Li, Y, Li, H, Li, J, Li, S, Lin, SM, López, FJ, Lu, X, Luo, H, Ma, X, Meehan, J, Megherbi, DB, Mei, N, Mu, B, Ning, B, Pandey, A, Pérez-Florido, J, Perkins, RG, Peters, R, Phan, JH, Pirooznia, M, Qian, F, Qing, T, Rainbow, L, Rocca-Serra, P, Sambourg, L, Sansone, SA, Schwartz, S, Shah, R, Shen, J, Smith, TM, Stegle, O, Stralis-Pavese, N, Stupka, E, Suzuki, Y, Szkotnicki, LT, Tinning, M, Tu, B, Van Delft, J, Vela-Boza, A, Venturini, E, Walker, SJ, Wan, L, Wang, W, Wang, J, Wang, J, Wieben, ED, Willey, JC, Wu, PY, Xuan, J, Yang, Y, Ye, Z, Yin, Y, Yu, Y, Yuan, YC, Zhang, J, Zhang, KK, Zhang, W, Zhang, W, Zhang, Y, Zhao, C, Zheng, Y, Zhou, Y, Zumbo, P, Tong, W, Kreil, DP, Mason, CE & Shi, L 2014, 'A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium', Nature Biotechnology, vol. 32, no. 9, pp. 903-914. https://doi.org/10.1038/nbt.2957
Su, Zhenqiang ; Łabaj, Paweł P. ; Li, Sheng ; Thierry-Mieg, Jean ; Thierry-Mieg, Danielle ; Shi, Wei ; Wang, Charles ; Schroth, Gary P. ; Setterquist, Robert A. ; Thompson, John F. ; Jones, Wendell D. ; Xiao, Wenzhong ; Xu, Weihong ; Jensen, Roderick V. ; Kelly, Reagan ; Xu, Joshua ; Conesa, Ana ; Furlanello, Cesare ; Gao, Hanlin ; Hong, Huixiao ; Jafari, Nadereh ; Letovsky, Stan ; Liao, Yang ; Lu, Fei ; Oakeley, Edward J. ; Peng, Zhiyu ; Praul, Craig A. ; Santoyo-Lopez, Javier ; Scherer, Andreas ; Shi, Tieliu ; Smyth, Gordon K. ; Staedtler, Frank ; Sykacek, Peter ; Tan, Xin Xing ; Thompson, E. Aubrey ; Vandesompele, Jo ; Wang, May D. ; Wang, Jian ; Wolfinger, Russell D. ; Zavadil, Jiri ; Auerbach, Scott S. ; Bao, Wenjun ; Binder, Hans ; Blomquist, Thomas ; Brilliant, Murray H. ; Bushel, Pierre R. ; Cai, Weimin ; Catalano, Jennifer G. ; Chang, Ching Wei ; Chen, Tao ; Chen, Geng ; Chen, Rong ; Chierici, Marco ; Chu, Tzu Ming ; Clevert, Djork Arné ; Deng, Youping ; Derti, Adnan ; Devanarayan, Viswanath ; Dong, Zirui ; Dopazo, Joaquin ; Du, Tingting ; Fang, Hong ; Fang, Yongxiang ; Fasold, Mario ; Fernandez, Anita ; Fischer, Matthias ; Furió-Tari, Pedro ; Fuscoe, James C. ; Caimet, Florian ; Gaj, Stan ; Gandara, Jorge ; Gao, Huan ; Ge, Weigong ; Gondo, Yoichi ; Gong, Binsheng ; Gong, Meihua ; Gong, Zhuolin ; Green, Bridgett ; Guo, Chao ; Guo, Lei ; Guo, Li Wu ; Hadfield, James ; Hellemans, Jan ; Hochreiter, Sepp ; Jia, Meiwen ; Jian, Min ; Johnson, Charles D. ; Kay, Suzanne ; Kleinjans, Jos ; Lababidi, Samir ; Levy, Shawn ; Li, Quan Zhen ; Li, Li ; Li, Li ; Li, Peng ; Li, Yan ; Li, Haiqing ; Li, Jianying ; Li, Shiyong ; Lin, Simon M. ; López, Francisco J. ; Lu, Xin ; Luo, Heng ; Ma, Xiwen ; Meehan, Joseph ; Megherbi, Dalila B. ; Mei, Nan ; Mu, Bing ; Ning, Baitang ; Pandey, Akhilesh ; Pérez-Florido, Javier ; Perkins, Roger G. ; Peters, Ryan ; Phan, John H. ; Pirooznia, Mehdi ; Qian, Feng ; Qing, Tao ; Rainbow, Lucille ; Rocca-Serra, Philippe ; Sambourg, Laure ; Sansone, Susanna Assunta ; Schwartz, Scott ; Shah, Ruchir ; Shen, Jie ; Smith, Todd M. ; Stegle, Oliver ; Stralis-Pavese, Nancy ; Stupka, Elia ; Suzuki, Yutaka ; Szkotnicki, Lee T. ; Tinning, Matthew ; Tu, Bimeng ; Van Delft, Joost ; Vela-Boza, Alicia ; Venturini, Elisa ; Walker, Stephen J. ; Wan, Liqing ; Wang, Wei ; Wang, Jinhui ; Wang, Jun ; Wieben, Eric D. ; Willey, James C. ; Wu, Po Yen ; Xuan, Jiekun ; Yang, Yong ; Ye, Zhan ; Yin, Ye ; Yu, Ying ; Yuan, Yate Ching ; Zhang, John ; Zhang, Ke K. ; Zhang, Wenqian ; Zhang, Wenwei ; Zhang, Yanyan ; Zhao, Chen ; Zheng, Yuanting ; Zhou, Yiming ; Zumbo, Paul ; Tong, Weida ; Kreil, David P. ; Mason, Christopher E. ; Shi, Leming. / A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. In: Nature Biotechnology. 2014 ; Vol. 32, No. 9. pp. 903-914.
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title = "A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium",
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.",
author = "Zhenqiang Su and Łabaj, {Paweł P.} and Sheng Li and Jean Thierry-Mieg and Danielle Thierry-Mieg and Wei Shi and Charles Wang and Schroth, {Gary P.} and Setterquist, {Robert A.} and Thompson, {John F.} and Jones, {Wendell D.} and Wenzhong Xiao and Weihong Xu and Jensen, {Roderick V.} and Reagan Kelly and Joshua Xu and Ana Conesa and Cesare Furlanello and Hanlin Gao and Huixiao Hong and Nadereh Jafari and Stan Letovsky and Yang Liao and Fei Lu and Oakeley, {Edward J.} and Zhiyu Peng and Praul, {Craig A.} and Javier Santoyo-Lopez and Andreas Scherer and Tieliu Shi and Smyth, {Gordon K.} and Frank Staedtler and Peter Sykacek and Tan, {Xin Xing} and Thompson, {E. Aubrey} and Jo Vandesompele and Wang, {May D.} and Jian Wang and Wolfinger, {Russell D.} and Jiri Zavadil and Auerbach, {Scott S.} and Wenjun Bao and Hans Binder and Thomas Blomquist and Brilliant, {Murray H.} and Bushel, {Pierre R.} and Weimin Cai and Catalano, {Jennifer G.} and Chang, {Ching Wei} and Tao Chen and Geng Chen and Rong Chen and Marco Chierici and Chu, {Tzu Ming} and Clevert, {Djork Arn{\'e}} and Youping Deng and Adnan Derti and Viswanath Devanarayan and Zirui Dong and Joaquin Dopazo and Tingting Du and Hong Fang and Yongxiang Fang and Mario Fasold and Anita Fernandez and Matthias Fischer and Pedro Furi{\'o}-Tari and Fuscoe, {James C.} and Florian Caimet and Stan Gaj and Jorge Gandara and Huan Gao and Weigong Ge and Yoichi Gondo and Binsheng Gong and Meihua Gong and Zhuolin Gong and Bridgett Green and Chao Guo and Lei Guo and Guo, {Li Wu} and James Hadfield and Jan Hellemans and Sepp Hochreiter and Meiwen Jia and Min Jian and Johnson, {Charles D.} and Suzanne Kay and Jos Kleinjans and Samir Lababidi and Shawn Levy and Li, {Quan Zhen} and Li Li and Li Li and Peng Li and Yan Li and Haiqing Li and Jianying Li and Shiyong Li and Lin, {Simon M.} and L{\'o}pez, {Francisco J.} and Xin Lu and Heng Luo and Xiwen Ma and Joseph Meehan and Megherbi, {Dalila B.} and Nan Mei and Bing Mu and Baitang Ning and Akhilesh Pandey and Javier P{\'e}rez-Florido and Perkins, {Roger G.} and Ryan Peters and Phan, {John H.} and Mehdi Pirooznia and Feng Qian and Tao Qing and Lucille Rainbow and Philippe Rocca-Serra and Laure Sambourg and Sansone, {Susanna Assunta} and Scott Schwartz and Ruchir Shah and Jie Shen and Smith, {Todd M.} and Oliver Stegle and Nancy Stralis-Pavese and Elia Stupka and Yutaka Suzuki and Szkotnicki, {Lee T.} and Matthew Tinning and Bimeng Tu and {Van Delft}, Joost and Alicia Vela-Boza and Elisa Venturini and Walker, {Stephen J.} and Liqing Wan and Wei Wang and Jinhui Wang and Jun Wang and Wieben, {Eric D.} and Willey, {James C.} and Wu, {Po Yen} and Jiekun Xuan and Yong Yang and Zhan Ye and Ye Yin and Ying Yu and Yuan, {Yate Ching} and John Zhang and Zhang, {Ke K.} and Wenqian Zhang and Wenwei Zhang and Yanyan Zhang and Chen Zhao and Yuanting Zheng and Yiming Zhou and Paul Zumbo and Weida Tong and Kreil, {David P.} and Mason, {Christopher E.} and Leming Shi",
year = "2014",
month = "9",
day = "1",
doi = "10.1038/nbt.2957",
language = "English (US)",
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pages = "903--914",
journal = "Biotechnology",
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TY - JOUR

T1 - A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

AU - Su, Zhenqiang

AU - Łabaj, Paweł P.

AU - Li, Sheng

AU - Thierry-Mieg, Jean

AU - Thierry-Mieg, Danielle

AU - Shi, Wei

AU - Wang, Charles

AU - Schroth, Gary P.

AU - Setterquist, Robert A.

AU - Thompson, John F.

AU - Jones, Wendell D.

AU - Xiao, Wenzhong

AU - Xu, Weihong

AU - Jensen, Roderick V.

AU - Kelly, Reagan

AU - Xu, Joshua

AU - Conesa, Ana

AU - Furlanello, Cesare

AU - Gao, Hanlin

AU - Hong, Huixiao

AU - Jafari, Nadereh

AU - Letovsky, Stan

AU - Liao, Yang

AU - Lu, Fei

AU - Oakeley, Edward J.

AU - Peng, Zhiyu

AU - Praul, Craig A.

AU - Santoyo-Lopez, Javier

AU - Scherer, Andreas

AU - Shi, Tieliu

AU - Smyth, Gordon K.

AU - Staedtler, Frank

AU - Sykacek, Peter

AU - Tan, Xin Xing

AU - Thompson, E. Aubrey

AU - Vandesompele, Jo

AU - Wang, May D.

AU - Wang, Jian

AU - Wolfinger, Russell D.

AU - Zavadil, Jiri

AU - Auerbach, Scott S.

AU - Bao, Wenjun

AU - Binder, Hans

AU - Blomquist, Thomas

AU - Brilliant, Murray H.

AU - Bushel, Pierre R.

AU - Cai, Weimin

AU - Catalano, Jennifer G.

AU - Chang, Ching Wei

AU - Chen, Tao

AU - Chen, Geng

AU - Chen, Rong

AU - Chierici, Marco

AU - Chu, Tzu Ming

AU - Clevert, Djork Arné

AU - Deng, Youping

AU - Derti, Adnan

AU - Devanarayan, Viswanath

AU - Dong, Zirui

AU - Dopazo, Joaquin

AU - Du, Tingting

AU - Fang, Hong

AU - Fang, Yongxiang

AU - Fasold, Mario

AU - Fernandez, Anita

AU - Fischer, Matthias

AU - Furió-Tari, Pedro

AU - Fuscoe, James C.

AU - Caimet, Florian

AU - Gaj, Stan

AU - Gandara, Jorge

AU - Gao, Huan

AU - Ge, Weigong

AU - Gondo, Yoichi

AU - Gong, Binsheng

AU - Gong, Meihua

AU - Gong, Zhuolin

AU - Green, Bridgett

AU - Guo, Chao

AU - Guo, Lei

AU - Guo, Li Wu

AU - Hadfield, James

AU - Hellemans, Jan

AU - Hochreiter, Sepp

AU - Jia, Meiwen

AU - Jian, Min

AU - Johnson, Charles D.

AU - Kay, Suzanne

AU - Kleinjans, Jos

AU - Lababidi, Samir

AU - Levy, Shawn

AU - Li, Quan Zhen

AU - Li, Li

AU - Li, Li

AU - Li, Peng

AU - Li, Yan

AU - Li, Haiqing

AU - Li, Jianying

AU - Li, Shiyong

AU - Lin, Simon M.

AU - López, Francisco J.

AU - Lu, Xin

AU - Luo, Heng

AU - Ma, Xiwen

AU - Meehan, Joseph

AU - Megherbi, Dalila B.

AU - Mei, Nan

AU - Mu, Bing

AU - Ning, Baitang

AU - Pandey, Akhilesh

AU - Pérez-Florido, Javier

AU - Perkins, Roger G.

AU - Peters, Ryan

AU - Phan, John H.

AU - Pirooznia, Mehdi

AU - Qian, Feng

AU - Qing, Tao

AU - Rainbow, Lucille

AU - Rocca-Serra, Philippe

AU - Sambourg, Laure

AU - Sansone, Susanna Assunta

AU - Schwartz, Scott

AU - Shah, Ruchir

AU - Shen, Jie

AU - Smith, Todd M.

AU - Stegle, Oliver

AU - Stralis-Pavese, Nancy

AU - Stupka, Elia

AU - Suzuki, Yutaka

AU - Szkotnicki, Lee T.

AU - Tinning, Matthew

AU - Tu, Bimeng

AU - Van Delft, Joost

AU - Vela-Boza, Alicia

AU - Venturini, Elisa

AU - Walker, Stephen J.

AU - Wan, Liqing

AU - Wang, Wei

AU - Wang, Jinhui

AU - Wang, Jun

AU - Wieben, Eric D.

AU - Willey, James C.

AU - Wu, Po Yen

AU - Xuan, Jiekun

AU - Yang, Yong

AU - Ye, Zhan

AU - Yin, Ye

AU - Yu, Ying

AU - Yuan, Yate Ching

AU - Zhang, John

AU - Zhang, Ke K.

AU - Zhang, Wenqian

AU - Zhang, Wenwei

AU - Zhang, Yanyan

AU - Zhao, Chen

AU - Zheng, Yuanting

AU - Zhou, Yiming

AU - Zumbo, Paul

AU - Tong, Weida

AU - Kreil, David P.

AU - Mason, Christopher E.

AU - Shi, Leming

PY - 2014/9/1

Y1 - 2014/9/1

N2 - 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.

AB - 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.

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U2 - 10.1038/nbt.2957

DO - 10.1038/nbt.2957

M3 - Article

VL - 32

SP - 903

EP - 914

JO - Biotechnology

JF - Biotechnology

SN - 0733-222X

IS - 9

ER -