Zhang, Wenqian, Yu, Ying, Hertwig, Falk, Thierry-Mieg, Jean, Zhang, Wenwei, Thierry-Mieg, Danielle ORCID: 0000-0001-9568-4211, Wang, Jian, Furlanello, Cesare, Devanarayan, Viswanath, Cheng, Jie, Deng, Youping, Hero, Barbara, Hong, Huixiao, Jia, Meiwen, Li, Li, Lin, Simon M., Nikolsky, Yuri, Oberthuer, Andre, Qing, Tao, Su, Zhenqiang, Volland, Ruth, Wang, Charles, Wang, May D., Ai, Junmei, Albanese, Davide ORCID: 0000-0002-9493-3850, Asgharzadeh, Shahab, Avigad, Smadar, Bao, Wenjun, Bessarabova, Marina, Brilliant, Murray H., Brors, Benedikt ORCID: 0000-0001-5940-3101, Chierici, Marco ORCID: 0000-0001-9791-9301, Chu, Tzu-Ming, Zhang, Jibin, Grundy, Richard G., He, Min Max, Hebbring, Scott, Kaufman, Howard L., Lababidi, Samir, Lancashire, Lee J., Li, Yan, Lu, Xin X., Luo, Heng ORCID: 0000-0001-5192-8878, Ma, Xiwen, Ning, Baitang, Noguera, Rosa, Peifer, Martin ORCID: 0000-0002-5243-5503, Phan, John H., Roels, Frederik, Rosswog, Carolina, Shao, Susan, Shen, Jie, Theissen, Jessica, Tonini, Gian Paolo, Vandesompele, Jo ORCID: 0000-0001-6274-0184, Wu, Po-Yen, Xiao, Wenzhong, Xu, Joshua, Xu, Weihong ORCID: 0000-0002-3988-3571, Xuan, Jiekun, Yang, Yong, Ye, Zhan, Dong, Zirui, Zhang, Ke K., Yin, Ye, Zhao, Chen, Zheng, Yuanting, Wolfinger, Russell D., Shi, Tieliu, Malkas, Linda H., Berthold, Frank, Wang, Jun ORCID: 0000-0002-2113-5874, Tong, Weida, Shi, Leming ORCID: 0000-0002-7143-2033, Peng, Zhiyu and Fischer, Matthias (2015). Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. Genome Biol., 16. LONDON: BMC. ISSN 1474-760X

Full text not available from this repository.

Abstract

Background: Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study for clinical endpoint prediction using neuroblastoma as a model. Results: We generate gene expression profiles from 498 primary neuroblastomas using both RNA-seq and 44 k microarrays. Characterization of the neuroblastoma transcriptome by RNA-seq reveals that more than 48,000 genes and 200,000 transcripts are being expressed in this malignancy. We also find that RNA-seq provides much more detailed information on specific transcript expression patterns in clinico-genetic neuroblastoma subgroups than microarrays. To systematically compare the power of RNA-seq and microarray-based models in predicting clinical endpoints, we divide the cohort randomly into training and validation sets and develop 360 predictive models on six clinical endpoints of varying predictability. Evaluation of factors potentially affecting model performances reveals that prediction accuracies are most strongly influenced by the nature of the clinical endpoint, whereas technological platforms (RNA-seq vs. microarrays), RNA-seq data analysis pipelines, and feature levels (gene vs. transcript vs. exon-junction level) do not significantly affect performances of the models. Conclusions: We demonstrate that RNA-seq outperforms microarrays in determining the transcriptomic characteristics of cancer, while RNA-seq and microarray-based models perform similarly in clinical endpoint prediction. Our findings may be valuable to guide future studies on the development of gene expression-based predictive models and their implementation in clinical practice.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Zhang, WenqianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yu, YingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hertwig, FalkUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Thierry-Mieg, JeanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhang, WenweiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Thierry-Mieg, DanielleUNSPECIFIEDorcid.org/0000-0001-9568-4211UNSPECIFIED
Wang, JianUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Furlanello, CesareUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Devanarayan, ViswanathUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Cheng, JieUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Deng, YoupingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hero, BarbaraUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hong, HuixiaoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jia, MeiwenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Li, LiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lin, Simon M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Nikolsky, YuriUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Oberthuer, AndreUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Qing, TaoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Su, ZhenqiangUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Volland, RuthUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wang, CharlesUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wang, May D.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ai, JunmeiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Albanese, DavideUNSPECIFIEDorcid.org/0000-0002-9493-3850UNSPECIFIED
Asgharzadeh, ShahabUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Avigad, SmadarUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Bao, WenjunUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Bessarabova, MarinaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Brilliant, Murray H.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Brors, BenediktUNSPECIFIEDorcid.org/0000-0001-5940-3101UNSPECIFIED
Chierici, MarcoUNSPECIFIEDorcid.org/0000-0001-9791-9301UNSPECIFIED
Chu, Tzu-MingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhang, JibinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Grundy, Richard G.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
He, Min MaxUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hebbring, ScottUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kaufman, Howard L.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lababidi, SamirUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lancashire, Lee J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Li, YanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lu, Xin X.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Luo, HengUNSPECIFIEDorcid.org/0000-0001-5192-8878UNSPECIFIED
Ma, XiwenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ning, BaitangUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Noguera, RosaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Peifer, MartinUNSPECIFIEDorcid.org/0000-0002-5243-5503UNSPECIFIED
Phan, John H.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Roels, FrederikUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Rosswog, CarolinaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Shao, SusanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Shen, JieUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Theissen, JessicaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tonini, Gian PaoloUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Vandesompele, JoUNSPECIFIEDorcid.org/0000-0001-6274-0184UNSPECIFIED
Wu, Po-YenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Xiao, WenzhongUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Xu, JoshuaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Xu, WeihongUNSPECIFIEDorcid.org/0000-0002-3988-3571UNSPECIFIED
Xuan, JiekunUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yang, YongUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ye, ZhanUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Dong, ZiruiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhang, Ke K.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Yin, YeUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zhao, ChenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zheng, YuantingUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wolfinger, Russell D.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Shi, TieliuUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Malkas, Linda H.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Berthold, FrankUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wang, JunUNSPECIFIEDorcid.org/0000-0002-2113-5874UNSPECIFIED
Tong, WeidaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Shi, LemingUNSPECIFIEDorcid.org/0000-0002-7143-2033UNSPECIFIED
Peng, ZhiyuUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fischer, MatthiasUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-400873
DOI: 10.1186/s13059-015-0694-1
Journal or Publication Title: Genome Biol.
Volume: 16
Date: 2015
Publisher: BMC
Place of Publication: LONDON
ISSN: 1474-760X
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
EXPRESSION-BASED CLASSIFICATION; GENE; SIGNATURE; REPRODUCIBILITY; TRANSCRIPTS; VALIDATION; PROFILESMultiple languages
Biotechnology & Applied Microbiology; Genetics & HeredityMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/40087

Downloads

Downloads per month over past year

Altmetric

Export

Actions (login required)

View Item View Item