Evidence map›Paper›PMID 26109056›Full record

ArticleGenome biology2015

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.

Wenqian Zhang, Ying Yu, Falk Hertwig, Jean Thierry-Mieg, Wenwei Zhang, Danielle Thierry-Mieg, Jian Wang, Cesare Furlanello, Viswanath Devanarayan, Jie Cheng and 66 more

Open access · hybridAbstract readComparative StudyEvaluation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 242 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
242citing papers in PubMed, 2 pooled it
11.6field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

242 citing papers in PubMed, 2 syntheses or guidelines pooled it, 426 citations in OpenAlex.

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182 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

76 authors at 20 institutions in 10 countries.

Wenqian ZhangBGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China.
Ying YuCollaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and School of Pharmacy, Fudan University, Shanghai, 201203, China.
Falk HertwigDepartment of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany.
Jean Thierry-MiegNIH/NCBI, Bldg 38A/Room 8S808, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
Wenwei ZhangBGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China.
Danielle Thierry-MiegNIH/NCBI, Bldg 38A/Room 8S808, 8600 Rockville Pike, Bethesda, MD, 20894, USA.
Jian WangEli Lilly and Company Research Informatics, Lilly Corporate Center, Drop Code 0725, Indianapolis, IN, 46285, USA.
Cesare FurlanelloFondazione Bruno Kessler (FBK), Via Sommarive 18, 38123, Trento Povo, TN, Italy.
Viswanath DevanarayanAbbVie Inc., Global Pharmaceutical R&D, 32 Knights Crest Court, Souderton, PA, 18964, USA.
Jie ChengGlaxoSmithKline, Discovery Analytics, Mailstop UP4335, 1250 South Collegeville Rd, Collegeville, PA, 19426, USA.
Youping DengDepartment of Internal Medicine, Rush University Cancer Center, 1725 W. Harrison Street, Chicago, IL, 60612, USA.
Barbara HeroDepartment of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany.
Huixiao HongNational Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA.
Meiwen JiaCollaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and School of Pharmacy, Fudan University, Shanghai, 201203, China.
Li LiSAS Institute Inc., SAS Campus Drive, Cary, NC, 27513, USA.
Simon M LinMarshfield Clinic Research Foundation, Biomedical Informatics Research Center, 1000 N Oak Avenue, Marshfield, WI, 54449, USA.
Yuri NikolskyThomson Reuters IP & Science, 5901 Priesty Drive, Carlsbad, CA, 92008, USA.
André OberthuerDepartment of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany.
Tao QingCollaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and School of Pharmacy, Fudan University, Shanghai, 201203, China.
Zhenqiang SuNational Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA.
Ruth VollandDepartment of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany.
Charles WangCenter for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA.
May D WangDepartment of Biomedical Engineering, GeorgiaTech and Emory University, 313 Ferst Drive, Atlanta, GA, 30332, USA.
Junmei AiDepartment of Internal Medicine, Rush University Cancer Center, 1725 W. Harrison Street, Chicago, IL, 60612, USA.
Davide AlbaneseFondazione Edmund Mach, CRI-CBC, San Michele all'Adige, TN, Italy.
Shahab AsgharzadehChildren's Hospital Los Angeles, Los Angeles, CA, 90027, USA.
Smadar AvigadDepartment of Pediatric Hematology-Oncology, Molecular Oncology, Felsenstein Medical Research Center, Schneider Children's Medical Center of Israel, Petach Tikva, 49202, Israel.
Wenjun BaoSAS Institute Inc., SAS Campus Drive, Cary, NC, 27513, USA.
Marina BessarabovaThomson Reuters IP & Science, 5901 Priesty Drive, Carlsbad, CA, 92008, USA.
Murray H BrilliantMarshfield Clinic Research Foundation, Center of Human Genetics, 1000 N Oak Avenue, Marshfield, WI, 54449, USA.
Benedikt BrorsDepartment of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120, Heidelberg, Germany.
Marco ChiericiFondazione Bruno Kessler (FBK), Via Sommarive 18, 38123, Trento Povo, TN, Italy.
Tzu-Ming ChuSAS Institute Inc., SAS Campus Drive, Cary, NC, 27513, USA.
Jibin ZhangBGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China.
Richard G GrundyUniversity of Nottingham, Children's Brain Tumour Research Centre, Queen's Medical Centre, University of Nottingham, D Floor Medical School, Nottingham, NG7 2UH, UK.
Min Max HeMarshfield Clinic Research Foundation, Biomedical Informatics Research Center, 1000 N Oak Avenue, Marshfield, WI, 54449, USA.
Scott HebbringMarshfield Clinic Research Foundation, Center of Human Genetics, 1000 N Oak Avenue, Marshfield, WI, 54449, USA.
Howard L KaufmanDepartment of Internal Medicine, Rush University Cancer Center, 1725 W. Harrison Street, Chicago, IL, 60612, USA.
Samir LababidiCenter for Biologics Evaluation and Research, U.S. Food and Drug Administration, WOC1 RM400S, HFM-210, 1401 Rockville Pike, Rockville, MD, 20852, USA.
Lee J LancashireThomson Reuters IP & Science, 5901 Priesty Drive, Carlsbad, CA, 92008, USA.
Yan LiDepartment of Internal Medicine, Rush University Cancer Center, 1725 W. Harrison Street, Chicago, IL, 60612, USA.
Xin X LuAbbVie Inc., Global Pharmaceutical Research and Development, 1 North Waukegan Road, North Chicago, IL, 60064, USA.
Heng LuoNational Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA.
Xiwen MaEli Lilly and Company, Discovery Statistics, Lilly Corporate Center, Drop Code 2036, Indianapolis, IN, 46285, USA.
Baitang NingNational Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA.
Rosa NogueraDepartment of Pathology, University of Valencia, Medical School, Avda. Blasco Ibáñez, 17, 46010, Valencia, Spain.
Martin PeiferUniversity of Cologne, Center for Molecular Medicine (CMMC), Medical Faculty, Kerpener Strasse 62, D-50924, Cologne, Germany.
John H PhanDepartment of Biomedical Engineering, GeorgiaTech and Emory University, 313 Ferst Drive, Atlanta, GA, 30332, USA.
Frederik RoelsDepartment of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany.
Carolina RosswogDepartment of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany.
Susan ShaoSAS Institute Inc., SAS Campus Drive, Cary, NC, 27513, USA.
Jie ShenNational Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA.
Jessica TheissenDepartment of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany.
Gian Paolo ToniniNeuroblastoma Laboratory, Onco/Hematology Laboratory, SDB Department, University of Padua, Pediatric Research Institute, Padua, Italy.
Jo VandesompeleDepartment of Pediatrics and Genetics, Ghent University, Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.
Po-Yen WuGeorgia Institute of Technology, School of Electrical and Computer Engineering, 777 Atlantic Drive NW, Atlanta, GA, 30332, USA.
Wenzhong XiaoHarvard Medical School, Massachusetts General Hospital, 51 Blossom Street, Boston, MA, 02114, USA.
Joshua XuNational Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA.
Weihong XuStanford University, Stanford Genome Technology Center, 855 South California Avenue, Palo Alto, CA, 94304, USA.
Jiekun XuanNational Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA.
Yong YangEli Lilly and Company Research Informatics, Lilly Corporate Center, Drop Code 0725, Indianapolis, IN, 46285, USA.
Zhan YeMarshfield Clinic Research Foundation, Biomedical Informatics Research Center, 1000 N Oak Avenue, Marshfield, WI, 54449, USA.
Zirui DongBGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China.
Ke K ZhangDepartment of Pathology, University of North Dakota School of Medicine, 501 N. Columbia Road RM 3573, Grand Forks, ND, 58202-9037, USA.
Ye YinBGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China.
Chen ZhaoCollaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and School of Pharmacy, Fudan University, Shanghai, 201203, China.
Yuanting ZhengCollaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and School of Pharmacy, Fudan University, Shanghai, 201203, China.
Russell D WolfingerSAS Institute Inc., SAS Campus Drive, Cary, NC, 27513, USA.
Tieliu ShiEast China Normal University, Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, 500 Dongchuan Road, Shanghai, 200241, China.
Linda H MalkasDepartment of Molecular & Cellular Biology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, 91010, USA.
Frank BertholdDepartment of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany.
Jun WangBGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China.
Weida TongNational Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA.
Leming ShiCollaborative Innovation Center for Genetics and Development, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences and School of Pharmacy, Fudan University, Shanghai, 201203, China. lemingshi@fudan.edu.cn.
Zhiyu PengBGI-Shenzhen, Main Building, Bei Shan Industrial Zone, Yantian District, Shenzhen, Guangdong, 518083, China. pengzhiyu@genomics.org.cn.
Matthias FischerDepartment of Pediatric Oncology and Hematology, University Children's Hospital of Cologne, Kerpener Strasse 62, D-50924, Cologne, Germany. matthias.fischer@uk-koeln.de.
University Hospital Cologne · DEBGI Group (China) · CNMarshfield Clinic · USSAS Institute (United States) · USUnited States Food and Drug Administration · USNational Center for Toxicological Research · USRush University · USState Key Laboratory of Genetic EngineeringThomson Reuters (United States) · USUniversity of Cologne · DEAbbVie (United States) · USEli Lilly (United States) · USFondazione Bruno Kessler · ITGeorgia Institute of Technology · USNational Center for Biotechnology Information · USBeckman Research InstituteBrain Tumour Research · GBChildren's Hospital of Los Angeles · USEast China Normal University · CNEmory University · US

Funding

WHOLE YEAST GENOME TRANSCRIPTIONAL AND FUNCTIONAL GENE MAPS--A FEASIBILITY STUDYP01HG000205 · NHGRI · STANFORD UNIVERSITY · PI DAVIS, RONALD WAYNE, HOWE, ROGER THOMAS · 1990 to 2016
$120.9M
Tissue and Animal UseU54CA119338 · NCI · EMORY UNIVERSITY · PI WANG, ZHONG · 2005 to 2009
$18.4M
Contrast-Enhanced and Image-Guided Surgery of Lung CancerR01CA163256 · NCI · EMORY UNIVERSITY · PI JO, HANJOONG, SINGHAL, SUNIL · 2011 to 2015
$6.5M
Nanotechnology for Multiplexed and Intraoperative Cancer DetectionRC2CA148265 · NCI · EMORY UNIVERSITY · PI NIE, SHUMING · 2009 to 2010
$2.0M
Protective behavioral strategies and mental health: Reducing alcohol-related riskR21AA020104 · NIAAA · LOYOLA MARYMOUNT UNIVERSITY · PI LABRIE, JOSEPH W. · 2010 to 2011
$367k
NCI NIH HHS 1RC2CA148265NCI NIH HHS R01 CA163256NCI NIH HHS R01CA163256NCI NIH HHS RC2 CA148265NCI NIH HHS U54 CA119338NCI NIH HHS U54CA119338NHGRI NIH HHS P01 HG000205NIAAA NIH HHS R21 AA020104
6 · The paper itself

Abstract

backgroundGene 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.

resultsWe 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.

conclusionsWe 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.

Indexed as

Gene Expression ProfilingOligonucleotide Array Sequence AnalysisSequence Analysis, RNAAdolescentAdultChildChild, PreschoolEndpoint DeterminationFemaleHumansInfantInfant, NewbornMaleModels, GeneticNeuroblastomaTumor Cells, Cultured

Identifiers

PMID26109056
PMCPMC4506430
OpenAlexW2124140824

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.