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Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data

  1. Author:
    Gao, Galen F
    Parker, Joel S
    Reynolds, Sheila M
    Silva, Tiago C
    Wang, Liang-Bo
    Zhou, Wanding
    Akbani, Rehan
    Bailey, Matthew
    Balu, Saianand
    Berman, Benjamin P
    Brooks, Denise
    Chen, Hu
    Cherniack, Andrew D
    Demchok, John A
    Ding, Li
    Felau, Ina
    Gaheen,Sharon
    Gerhard, Daniela S
    Heiman, David I
    Hernandez, Kyle M
    Hoadley, Katherine A
    Jayasinghe, Reyka
    Kemal, Anab
    Knijnenburg, Theo A
    Laird, Peter W
    Mensah, Michael K A
    Mungall, Andrew J
    Robertson, A Gordon
    Shen, Hui
    Tarnuzzer, Roy
    Wang, Zhining
    Wyczalkowski, Matthew
    Yang, Liming
    Zenklusen, Jean C
    Zhang, Zhenyu
    Liang, Han
    Noble, Michael S

  2. Author Address

    Eli 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., Department of Genetics, Lineberger Comprehensive Cancer Center, the University of North Carolin at Chapel Hill, Chapel Hill, NC 27599, USA., Institute for Systems Biology, Seattle, WA 98109, USA., Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Genetics, Ribeir 227;o Preto Medical School, University of S 227;o Paulo, Ribeir 227;o Preto, SP 14.040-905, Brazil., Department 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., Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA., Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA., Lineberger Comprehensive Cancer Center, Bioinformatics Core, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA., Center 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., Canada 39;s Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada., Department 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., Eli 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., National Cancer Institute, Bethesda, MD 20892, USA., Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA., Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA., Department of Pediatrics, the University of Chicago, Chicago, IL 60637, USA; Center for Research Informatics, the University of Chicago, Chicago, IL 60637, USA., Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA., Center for Translational Data Science, the University of Chicago, Chicago, IL 60615, USA., Department 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., Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA. Electronic address: mnoble@cogenimmune.com.,
    1. Year: 2019
    2. Date: Jul 24
  2. Journal: Cell systems
    1. 9
    2. 1
    3. Pages: 24-34.e10
  4. Type of Article: Article
  5. ISSN: 2405-4712
  1. 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. Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.

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External Sources

  1. View Full Text
  2. DOI: 10.1016/j.cels.2019.06.006
  3. PMID: 31344359
  4. View record in Web of Science®
  5. WOS: 000483321900004
  6. PII : S2405-4712(19)30201-7

Library Notes

  1. Fiscal Year: FY2018-2019
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