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Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data.
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.
Afiliación
  • Gao GF; 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.
  • Parker JS; Department of Genetics, Lineberger Comprehensive Cancer Center, the University of North Carolin at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Reynolds SM; Institute for Systems Biology, Seattle, WA 98109, USA.
  • Silva TC; Center 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.
  • Wang LB; 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.
  • Zhou W; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
  • Akbani R; Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
  • Bailey M; 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.
  • Balu S; Lineberger Comprehensive Cancer Center, Bioinformatics Core, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Berman BP; 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.
  • Brooks D; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.
  • Chen H; 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.
  • Cherniack AD; 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.
  • Demchok JA; National Cancer Institute, Bethesda, MD 20892, USA.
  • Ding L; 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.
  • Felau I; National Cancer Institute, Bethesda, MD 20892, USA.
  • Gaheen S; Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA.
  • Gerhard DS; National Cancer Institute, Bethesda, MD 20892, USA.
  • Heiman DI; Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.
  • Hernandez KM; Department of Pediatrics, the University of Chicago, Chicago, IL 60637, USA; Center for Research Informatics, the University of Chicago, Chicago, IL 60637, USA.
  • Hoadley KA; Department of Genetics, Lineberger Comprehensive Cancer Center, the University of North Carolin at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Jayasinghe R; Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA.
  • Kemal A; National Cancer Institute, Bethesda, MD 20892, USA.
  • Knijnenburg TA; Institute for Systems Biology, Seattle, WA 98109, USA.
  • Laird PW; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
  • Mensah MKA; National Cancer Institute, Bethesda, MD 20892, USA.
  • Mungall AJ; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.
  • Robertson AG; Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.
  • Shen H; Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.
  • Tarnuzzer R; National Cancer Institute, Bethesda, MD 20892, USA.
  • Wang Z; National Cancer Institute, Bethesda, MD 20892, USA.
  • Wyczalkowski M; 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.
  • Yang L; National Cancer Institute, Bethesda, MD 20892, USA.
  • Zenklusen JC; National Cancer Institute, Bethesda, MD 20892, USA.
  • Zhang Z; Center for Translational Data Science, the University of Chicago, Chicago, IL 60615, USA.
  • Liang H; 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 Texa
  • Noble MS; Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA. Electronic address: mnoble@cogenimmune.com.
Cell Syst ; 9(1): 24-34.e10, 2019 07 24.
Article en En | MEDLINE | ID: mdl-31344359
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.
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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Programas Informáticos / Genoma / MicroARNs / Neoplasias Límite: Humans Idioma: En Revista: Cell Syst Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
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Buscar en Google

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Programas Informáticos / Genoma / MicroARNs / Neoplasias Límite: Humans Idioma: En Revista: Cell Syst Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos