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

Controlled Before-After Studies Datasets as Topic Gene Expression Profiling Genome / genetics Genome, Human Genomics Health Information Exchange High-Throughput Nucleotide Sequencing Humans MicroRNAs / genetics Molecular Sequence Annotation Neoplasms / genetics Reproducibility of Results Software
DNA methylation The Cancer Genome Atlas human reference genome mRNA expression microRNA expression quality control somatic copy number alteration somatic mutation

Journal

Cell systems
ISSN: 2405-4720
Titre abrégé: Cell Syst
Pays: United States
ID NLM: 101656080

Informations de publication

Date de publication:
24 07 2019
Historique:
received: 19 01 2019
revised: 18 03 2019
accepted: 13 06 2019
entrez: 26 7 2019
pubmed: 26 7 2019
medline: 31 7 2020
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1016/j.cels.2019.06.006 PMID: 31344359 PMC: PMC6707074
pubmed: 31344359
pii: S2405-4712(19)30201-7
doi: 10.1016/j.cels.2019.06.006
pmc: PMC6707074
mid: NIHMS1535521
pii:
doi:

Substances chimiques

MicroRNAs 0

Types de publication

Comparative Study Journal Article Research Support, N.I.H., Extramural

Langues

eng

Sous-ensembles de citation

IM

Pagination

24-34.e10

Subventions

Organisme : NCI NIH HHS
ID : U24 CA210978
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210950
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210974
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210989
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210952
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210957
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA175486
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210949
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA209851
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210990
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA211000
Pays : United States
Organisme : NIEHS NIH HHS
ID : P30 ES010126
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA016672
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210969
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210988
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA143883
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA211006
Pays : United States
Organisme : NCI NIH HHS
ID : U24 CA210999
Pays : United States

Informations de copyright

Copyright © 2019 The Authors. Published by Elsevier Inc. All rights reserved.

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Auteurs

Galen F 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.

Joel S Parker (JS)

Department of Genetics, Lineberger Comprehensive Cancer Center, the University of North Carolin at Chapel Hill, Chapel Hill, NC 27599, USA.

Sheila M Reynolds (SM)

Institute for Systems Biology, Seattle, WA 98109, USA.

Tiago C 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.

Liang-Bo 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.

Wanding Zhou (W)

Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.

Rehan Akbani (R)

Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.

Matthew 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.

Saianand Balu (S)

Lineberger Comprehensive Cancer Center, Bioinformatics Core, the University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.

Benjamin P 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.

Denise Brooks (D)

Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.

Hu 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.

Andrew D 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.

John A Demchok (JA)

National Cancer Institute, Bethesda, MD 20892, USA.

Li 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.

Ina Felau (I)

National Cancer Institute, Bethesda, MD 20892, USA.

Sharon Gaheen (S)

Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA.

Daniela S Gerhard (DS)

National Cancer Institute, Bethesda, MD 20892, USA.

David I Heiman (DI)

Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA.

Kyle M 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.

Katherine A Hoadley (KA)

Department of Genetics, Lineberger Comprehensive Cancer Center, the University of North Carolin at Chapel Hill, Chapel Hill, NC 27599, USA.

Reyka Jayasinghe (R)

Department of Medicine, Washington University in St Louis, Saint Louis, MO 63108, USA.

Anab Kemal (A)

National Cancer Institute, Bethesda, MD 20892, USA.

Theo A Knijnenburg (TA)

Institute for Systems Biology, Seattle, WA 98109, USA.

Peter W Laird (PW)

Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.

Michael K A Mensah (MKA)

National Cancer Institute, Bethesda, MD 20892, USA.

Andrew J Mungall (AJ)

Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.

A Gordon Robertson (AG)

Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.

Hui Shen (H)

Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA.

Roy Tarnuzzer (R)

National Cancer Institute, Bethesda, MD 20892, USA.

Zhining Wang (Z)

National Cancer Institute, Bethesda, MD 20892, USA.

Matthew 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.

Liming Yang (L)

National Cancer Institute, Bethesda, MD 20892, USA.

Jean C Zenklusen (JC)

National Cancer Institute, Bethesda, MD 20892, USA.

Zhenyu Zhang (Z)

Center for Translational Data Science, the University of Chicago, Chicago, IL 60615, USA.

Han 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 Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: hliang1@mdanderson.org.

Michael S 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.

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Classifications MeSH

questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Caractéristiques des études épidémiologiques › Études épidémiologiques › Études contrôlées avant-après › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Collecte de données › Jeux de données comme sujet › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de profil d'expression de gènes › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome humain › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Disciplines des sciences naturelles › Disciplines des sciences biologiques › Biologie › Génétique › Génomique › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Sciences de l'information › Gestion de l'information › Gestion de l'information en santé › Échange d'informations de santé › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de séquence › Séquençage nucléotidique à haut débit › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › Petit ARN non traduit › microARN › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Annotation de séquence moléculaire › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Tumeurs › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Méthodologie en recherche épidémiologique › Reproductibilité des résultats › Before and After: Comparison of Legacy and...
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › Before and After: Comparison of Legacy and...