Su, Zhenqiang, Labaj, Pawel P., Li, Sheng, Thierry-Mieg, Jean, Thierry-Mieg, Danielle ORCID: 0000-0001-9568-4211, Shi, Wei, Wang, Charles, Schroth, Gary P., Setterquist, Robert A., Thompson, John F., Jones, Wendell D., Xiao, Wenzhong, Xu, Weihong ORCID: 0000-0002-3988-3571, 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 ORCID: 0000-0003-2349-750X, Praul, Craig A., Santoyo-Lopez, Javier ORCID: 0000-0003-1988-5059, Scherer, Andreas, Shi, Tieliu, Smyth, Gordon K., Staedtler, Frank, Sykacek, Peter, Tan, Xin-Xing, Thompson, E. Aubrey, Vandesompele, Jo ORCID: 0000-0001-6274-0184, Wang, May D., Wang, Jian, Wolfinger, Russell D., Zavadil, Jiri ORCID: 0000-0003-0640-5562, Auerbach, Scott S., Bao, Wenjun, Binder, Hans, Blomquist, Thomas, Brilliant, Murray H., Bushel, Pierre R., Cain, Weimin, Catalano, Jennifer G., Chang, Ching-Wei, Chen, Tao, Chen, Geng, Chen, Rong, Chierici, Marco ORCID: 0000-0001-9791-9301, Chu, Tzu-Ming, Clevert, Djork-Arne ORCID: 0000-0003-4191-2156, Deng, Youping, Derti, Adnan, Devanarayan, Viswanath, Dong, Zirui, Dopazo, Joaquin, Du, Tingting, Fang, Hong, Fang, Yongxiang, Fasold, Mario, Fernandez, Anita, Fischer, Matthias, Furio-Tari, Pedro, Fuscoe, James C., Caiment, Florian ORCID: 0000-0002-3325-0466, Gaj, Stan, Gandara, Jorge, Gao, Huan, Ge, Weigong, Gondo, Yoichi ORCID: 0000-0003-2184-6489, Gong, Binsheng ORCID: 0000-0002-8724-5435, Gong, Meihua, Gong, Zhuolin, Green, Bridgett, Guo, Chao ORCID: 0000-0002-6673-0933, Guo, Lei, Guo, Li-Wu, Hadfield, James, Hellemans, Jan, Hochreiter, Sepp ORCID: 0000-0001-7449-2528, Jia, Meiwen, Jian, Min, Johnson, Charles D., Kay, Suzanne, Kleinjans, Jos, Lababidi, Samir, Levy, Shawn ORCID: 0000-0002-1369-5740, Li, Quan-Zhen, Li, Li, Li, Li, Li, Peng, Li, Yan, Li, Haiqing, Li, Jianying, Li, Shiyong, Lin, Simon M., Lopez, Francisco J., Lu, Xin, Luo, Heng ORCID: 0000-0001-5192-8878, Ma, Xiwen, Meehan, Joseph, Megherbi, Dalila B., Mei, Nan ORCID: 0000-0002-3501-9014, Mu, Bing, Ning, Baitang, Pandey, Akhilesh, Perez-Florido, Javier, Perkins, Roger G., Peters, Ryan, Phan, John H., Pirooznia, Mehdi ORCID: 0000-0002-4210-6458, Qian, Feng, Qing, Tao, Rainbow, Lucille, Rocca-Serra, Philippe, Sambourg, Laure, Sansone, Susanna-Assunta ORCID: 0000-0001-5306-5690, Schwartz, Scott, Shah, Ruchir, Shen, Jie, Smith, Todd M., Stegle, Oliver ORCID: 0000-0002-8818-7193, Stralis-Pavese, Nancy, Stupka, Elia ORCID: 0000-0003-3154-4011, Suzuki, Yutaka, Szkotnicki, Lee T., Tinning, Matthew, Tu, Bimeng, van Deft, Joost, Vela-Boza, Alicia, Venturini, Elisa, Walker, Stephen J., Wan, Liqing, Wang, Wei, Wang, Jinhui, Wang, Jun ORCID: 0000-0002-8540-8931, 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 ORCID: 0000-0001-7801-0215, Zhao, Chen, Zheng, Yuanting, Zhou, Yiming, Zumbo, Paul, Tong, Weida, Kreil, David P., Mason, Christopher E. and Shi, Leming ORCID: 0000-0002-7143-2033 (2014). A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat. Biotechnol., 32 (9). S. 903 - 915. NEW YORK: NATURE PUBLISHING GROUP. ISSN 1546-1696

Full text not available from this repository.

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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Su, ZhenqiangUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Labaj, Pawel P.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Li, ShengUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Thierry-Mieg, JeanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Thierry-Mieg, DanielleUNSPECIFIEDorcid.org/0000-0001-9568-4211UNSPECIFIED
Shi, WeiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wang, CharlesUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schroth, Gary P.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Setterquist, Robert A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Thompson, John F.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jones, Wendell D.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Xiao, WenzhongUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Xu, WeihongUNSPECIFIEDorcid.org/0000-0002-3988-3571UNSPECIFIED
Jensen, Roderick V.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kelly, ReaganUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Xu, JoshuaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Conesa, AnaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Furlanello, CesareUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gao, HanlinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hong, HuixiaoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jafari, NaderehUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Letovsky, StanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Liao, YangUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lu, FeiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Oakeley, Edward J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Peng, ZhiyuUNSPECIFIEDorcid.org/0000-0003-2349-750XUNSPECIFIED
Praul, Craig A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Santoyo-Lopez, JavierUNSPECIFIEDorcid.org/0000-0003-1988-5059UNSPECIFIED
Scherer, AndreasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Shi, TieliuUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Smyth, Gordon K.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Staedtler, FrankUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sykacek, PeterUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tan, Xin-XingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Thompson, E. AubreyUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Vandesompele, JoUNSPECIFIEDorcid.org/0000-0001-6274-0184UNSPECIFIED
Wang, May D.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wang, JianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wolfinger, Russell D.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zavadil, JiriUNSPECIFIEDorcid.org/0000-0003-0640-5562UNSPECIFIED
Auerbach, Scott S.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Bao, WenjunUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Binder, HansUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Blomquist, ThomasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Brilliant, Murray H.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Bushel, Pierre R.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Cain, WeiminUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Catalano, Jennifer G.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chang, Ching-WeiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chen, TaoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chen, GengUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chen, RongUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Chierici, MarcoUNSPECIFIEDorcid.org/0000-0001-9791-9301UNSPECIFIED
Chu, Tzu-MingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Clevert, Djork-ArneUNSPECIFIEDorcid.org/0000-0003-4191-2156UNSPECIFIED
Deng, YoupingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Derti, AdnanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Devanarayan, ViswanathUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Dong, ZiruiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Dopazo, JoaquinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Du, TingtingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fang, HongUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fang, YongxiangUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fasold, MarioUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fernandez, AnitaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fischer, MatthiasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Furio-Tari, PedroUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fuscoe, James C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Caiment, FlorianUNSPECIFIEDorcid.org/0000-0002-3325-0466UNSPECIFIED
Gaj, StanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gandara, JorgeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gao, HuanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ge, WeigongUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gondo, YoichiUNSPECIFIEDorcid.org/0000-0003-2184-6489UNSPECIFIED
Gong, BinshengUNSPECIFIEDorcid.org/0000-0002-8724-5435UNSPECIFIED
Gong, MeihuaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gong, ZhuolinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Green, BridgettUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Guo, ChaoUNSPECIFIEDorcid.org/0000-0002-6673-0933UNSPECIFIED
Guo, LeiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Guo, Li-WuUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hadfield, JamesUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hellemans, JanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hochreiter, SeppUNSPECIFIEDorcid.org/0000-0001-7449-2528UNSPECIFIED
Jia, MeiwenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jian, MinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Johnson, Charles D.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kay, SuzanneUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kleinjans, JosUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lababidi, SamirUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Levy, ShawnUNSPECIFIEDorcid.org/0000-0002-1369-5740UNSPECIFIED
Li, Quan-ZhenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Li, LiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Li, LiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Li, PengUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Li, YanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Li, HaiqingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Li, JianyingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Li, ShiyongUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lin, Simon M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lopez, Francisco J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lu, XinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Luo, HengUNSPECIFIEDorcid.org/0000-0001-5192-8878UNSPECIFIED
Ma, XiwenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Meehan, JosephUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Megherbi, Dalila B.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Mei, NanUNSPECIFIEDorcid.org/0000-0002-3501-9014UNSPECIFIED
Mu, BingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ning, BaitangUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pandey, AkhileshUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Perez-Florido, JavierUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Perkins, Roger G.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Peters, RyanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Phan, John H.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Pirooznia, MehdiUNSPECIFIEDorcid.org/0000-0002-4210-6458UNSPECIFIED
Qian, FengUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Qing, TaoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Rainbow, LucilleUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Rocca-Serra, PhilippeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sambourg, LaureUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Sansone, Susanna-AssuntaUNSPECIFIEDorcid.org/0000-0001-5306-5690UNSPECIFIED
Schwartz, ScottUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Shah, RuchirUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Shen, JieUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Smith, Todd M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Stegle, OliverUNSPECIFIEDorcid.org/0000-0002-8818-7193UNSPECIFIED
Stralis-Pavese, NancyUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Stupka, EliaUNSPECIFIEDorcid.org/0000-0003-3154-4011UNSPECIFIED
Suzuki, YutakaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Szkotnicki, Lee T.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tinning, MatthewUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tu, BimengUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
van Deft, JoostUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Vela-Boza, AliciaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Venturini, ElisaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Walker, Stephen J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wan, LiqingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wang, WeiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wang, JinhuiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wang, JunUNSPECIFIEDorcid.org/0000-0002-8540-8931UNSPECIFIED
Wieben, Eric D.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Willey, James C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wu, Po-YenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Xuan, JiekunUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yang, YongUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ye, ZhanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yin, YeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yu, YingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yuan, Yate-ChingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhang, JohnUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhang, Ke K.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhang, WenqianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhang, WenweiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhang, YanyanUNSPECIFIEDorcid.org/0000-0001-7801-0215UNSPECIFIED
Zhao, ChenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zheng, YuantingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhou, YimingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zumbo, PaulUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tong, WeidaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kreil, David P.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Mason, Christopher E.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Shi, LemingUNSPECIFIEDorcid.org/0000-0002-7143-2033UNSPECIFIED
URN: urn:nbn:de:hbz:38-431337
DOI: 10.1038/nbt.2957
Journal or Publication Title: Nat. Biotechnol.
Volume: 32
Number: 9
Page Range: S. 903 - 915
Date: 2014
Publisher: NATURE PUBLISHING GROUP
Place of Publication: NEW YORK
ISSN: 1546-1696
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
DIFFERENTIAL GENE-EXPRESSION; GENOME ANNOTATION; TRANSCRIPTOME; ARRAYS; BIAS; PCRMultiple languages
Biotechnology & Applied MicrobiologyMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/43133

Downloads

Downloads per month over past year

Altmetric

Export

Actions (login required)

View Item View Item