ArticleCell systems2019
Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data.
Abstract readComparative Study
In one paragraph
Article in Cell systems, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers, 4 of them syntheses that pooled it.
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99citing papers in PubMed, 4 pooled it
–field-weighted citation impact
What it found
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The trial behind it
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Who cites it
99 citing papers in PubMed, 4 syntheses or guidelines pooled it.
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- Precision medicine for epilepsy: challenges and perspectives for an optimized clinical care pathway.Frontiers in neurology · 2025Review
- A comparative analysis of gene expression profiling by statistical and machine learning approaches.Bioinformatics advances · 2025Article
39 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
38 authors.
Galen F GaoEli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; The University of Texas Southwestern Medical School, Dallas, TX 75390, USA.
Joel S ParkerDepartment of Genetics, Lineberger Comprehensive Cancer Center, the University of North Carolin at Chapel Hill, Chapel Hill, NC 27599, USA.
Sheila M ReynoldsInstitute for Systems Biology, Seattle, WA 98109, USA.
Tiago C SilvaCenter for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14.040-905, Brazil.
Liang-Bo WangDepartment of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St Louis, Saint Louis, MO 63108, USA.
Wanding ZhouCenter for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
Rehan AkbaniDepartment of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Matthew BaileyDepartment of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St Louis, Saint Louis, MO 63108, USA.
Saianand BaluLineberger Comprehensive Cancer Center, Bioinformatics Core, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Benjamin P BermanCenter for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Faculty of Medicine, Department of Developmental Biology and Cancer Research, the Hebrew University of Jerusalem, Jerusalem 91120, Israel.
Denise BrooksCanada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.
Hu ChenDepartment of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA.
Andrew D CherniackEli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
John A DemchokNational Cancer Institute, Bethesda, MD 20892, USA.
Li DingDepartment of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St Louis, Saint Louis, MO 63108, USA.
Ina FelauNational Cancer Institute, Bethesda, MD 20892, USA.
Sharon GaheenFrederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA.
Daniela S GerhardNational Cancer Institute, Bethesda, MD 20892, USA.
David I HeimanEli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
Kyle M HernandezDepartment of Pediatrics, the University of Chicago, Chicago, IL 60637, USA; Center for Research Informatics, the University of Chicago, Chicago, IL 60637, USA.
Katherine A HoadleyDepartment of Genetics, Lineberger Comprehensive Cancer Center, the University of North Carolin at Chapel Hill, Chapel Hill, NC 27599, USA.
Reyka JayasingheDepartment of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA.
Anab KemalNational Cancer Institute, Bethesda, MD 20892, USA.
Theo A KnijnenburgInstitute for Systems Biology, Seattle, WA 98109, USA.
Peter W LairdCenter for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
Michael K A MensahNational Cancer Institute, Bethesda, MD 20892, USA.
Andrew J MungallCanada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.
A Gordon RobertsonCanada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.
Hui ShenCenter for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
Roy TarnuzzerNational Cancer Institute, Bethesda, MD 20892, USA.
Zhining WangNational Cancer Institute, Bethesda, MD 20892, USA.
Matthew WyczalkowskiDepartment of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA; McDonnell Genome Institute, Washington University in St Louis, Saint Louis, MO 63108, USA; Siteman Cancer Center, Washington University in St Louis, Saint Louis, MO 63108, USA.
Liming YangNational Cancer Institute, Bethesda, MD 20892, USA.
Jean C ZenklusenNational Cancer Institute, Bethesda, MD 20892, USA.
Zhenyu ZhangCenter for Translational Data Science, the University of Chicago, Chicago, IL 60615, USA.
Genomic Data Analysis Network
Han LiangDepartment of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; Department of Systems Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: hliang1@mdanderson.org.
Michael S NobleEli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA. Electronic address: mnoble@cogenimmune.com.
Funding
Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Fabien Delerue · 1985 to 2026
$290.8MUNC-CH CENTER FOR ENVIRONMENTAL HEALTH &SUSCEPTIBILITYP30ES010126 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Stephanie Engel · 2001 to 2026
$36.3MIntegrative Pipeline for Analysis & Translational Application of TCGA Data (GDAC)U24CA143883 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI AKBANI, REHAN, MILLS, GORDON B. · 2009 to 2016
$10.6MGlobal Infrastructure for Collaborative High-throughput Cancer Genomics AnalysisU24CA210999 · NCI · BROAD INSTITUTE, INC. · PI GETZ, GAD A · 2016 to 2020
$4.7MVisualization hub for genomics data exploration and translational discoveryU24CA210974 · NCI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI COLLISSON, ERIC, HAUSSLER, DAVID H · 2016 to 2020
$4.2MTCPA: an Integrated Bioinformatics Resource for Functional Cancer Proteomic DataU24CA209851 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI LIANG, HAN, MILLS, GORDON B. · 2016 to 2020
$4.0MIntegrative Cancer Epigenomic Data Analysis Center (ICE-DAC)U24CA210969 · NCI · VAN ANDEL RESEARCH INSTITUTE · PI LAIRD, PETER W · 2016 to 2020
$2.5MThe joint WCM-NYGC Center for Functional and Clinical Interpretation of Tumor ProfilesU24CA210989 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI ELEMENTO, OLIVIER, ZODY, MICHAEL C · 2016 to 2020
$2.4MCenter for the comprehensive analysis of somatic copy-number alterations in cancerU24CA210978 · NCI · BROAD INSTITUTE, INC. · PI BEROUKHIM, RAMEEN, CHERNIACK, ANDREW DAVID · 2016 to 2020
$2.3MUCSC-Buck Specialized Genomic Data Analysis Center for the Genomic Data Analysis NetworkU24CA210990 · NCI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI STUART, JOSHUA MICHAEL · 2016 to 2020
$2.2MOHSU Center for Specialized Data Analysis as part of the GDANU24CA210957 · NCI · OREGON HEALTH & SCIENCE UNIVERSITY · PI DEMIR, EMEK, SPELLMAN, PAUL T. · 2016 to 2020
$2.2MRNA sequencing analysis of CancerU24CA210988 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAYES, DAVID N, HOADLEY, KATHERINE A. · 2016 to 2020
$2.1MNCI NIH HHS P30 CA016672NCI NIH HHS R01 CA175486NCI NIH HHS U24 CA143883NCI NIH HHS U24 CA209851NCI NIH HHS U24 CA210949NCI NIH HHS U24 CA210950NCI NIH HHS U24 CA210952NCI NIH HHS U24 CA210957NCI NIH HHS U24 CA210969NCI NIH HHS U24 CA210974NCI NIH HHS U24 CA210978NCI NIH HHS U24 CA210988NCI NIH HHS U24 CA210989NCI NIH HHS U24 CA210990NCI NIH HHS U24 CA210999NCI NIH HHS U24 CA211000NCI NIH HHS U24 CA211006NIEHS NIH HHS P30 ES010126
Abstract
We present a systematic analysis of the effects of synchronizing a large-scale, deeply characterized, multi-omic dataset to the current human reference genome, using updated software, pipelines, and annotations. For each of 5 molecular data platforms in The Cancer Genome Atlas (TCGA)-mRNA and miRNA expression, single nucleotide variants, DNA methylation and copy number alterations-comprehensive sample, gene, and probe-level studies were performed, towards quantifying the degree of similarity between the 'legacy' GRCh37 (hg19) TCGA data and its GRCh38 (hg38) version as 'harmonized' by the Genomic Data Commons. We offer gene lists to elucidate differences that remained after controlling for confounders, and strategies to mitigate their impact on biological interpretation. Our results demonstrate that the hg19 and hg38 TCGA datasets are very highly concordant, promote informed use of either legacy or harmonized omics data, and provide a rubric that encourages similar comparisons as new data emerge and reference data evolve.
Indexed as
SoftwareControlled Before-After StudiesDatasets as TopicGene Expression ProfilingGenomeGenome, HumanGenomicsHealth Information ExchangeHigh-Throughput Nucleotide SequencingHumansMicroRNAsMolecular Sequence AnnotationNeoplasmsReproducibility of ResultsMicroRNAsDNA methylationhuman reference genomemicroRNA expressionmRNA expressionquality controlsomatic copy number alterationsomatic mutationThe Cancer Genome Atlas
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