Evidence map›Paper›PMID 29625055›Full record

ArticleCell2018

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics.

Jianfang Liu, Tara Lichtenberg, Katherine A Hoadley, Laila M Poisson, Alexander J Lazar, Andrew D Cherniack, Albert J Kovatich, Christopher C Benz, Douglas A Levine, Adrian V Lee and 6 more

Abstract read
In one paragraph

Article in Cell, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2,494 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
2,494citing papers in PubMed, 2 pooled it
–field-weighted citation impact
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

2,494 citing papers in PubMed, 2 syntheses or guidelines pooled it.

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  18. Cancers · 2026
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2,434 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

16 authors.

Jianfang LiuChan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA.
Tara LichtenbergNationwide Children's Hospital, Columbus, OH 43205, USA.
Katherine A HoadleyDepartment of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Laila M PoissonHenry Ford Cancer Institute and Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI 48202, USA.
Alexander J LazarDepartments of Pathology, Genomic Medicine, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Andrew D CherniackThe Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
Albert J KovatichClinical Breast Care Project, Murtha Cancer Center, Uniformed Services University/Walter Reed National Military Medical Center, Bethesda, MD 20889, USA.
Christopher C BenzBuck Institute for Research on Aging, Novato, CA 94945, USA.
Douglas A LevineDivision of Gynecologic Oncology, Department of OB/GYN, NYU Langone Medical Center, New York, NY 10016, USA.
Adrian V LeeDepartment of Pharmacology and Chemical Biology and Human Genetics, University of Pittsburgh, Women's Cancer Research Center, UPMC Hillman Cancer Center and Magee-Womens Research Institute, Pittsburgh, PA 15213, USA.
Larsson OmbergSage Bionetworks, Seattle, WA 98109, USA.
Denise M WolfDepartment of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
Craig D ShriverMurtha Cancer Center, Uniformed Services University/Walter Reed National Military Medical Center, Bethesda, MD 20889, USA.
Vesteinn ThorssonInstitute for Systems Biology, Seattle, WA 98109, USA.
Cancer Genome Atlas Research Network
Hai HuChan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA 15963, USA. Electronic address: h.hu@wriwindber.org.

Funding

Large Scale Sequencing and Analysis of GenomesU54HG003067 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI GABRIEL, STACEY, LANDER, ERIC S · 2004 to 2015
$568.6M
Large Scale Genome SequencingU54HG003079 · NHGRI · WASHINGTON UNIVERSITY · PI DUTCHER, SUSAN K · 2004 to 2016
$445.7M
The Human Genome Sequencing CenterU54HG003273 · NHGRI · BAYLOR COLLEGE OF MEDICINE · PI GIBBS, RICHARD A · 2004 to 2015
$341.3M
Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI Scott Kopetz · 1985 to 2026
$290.8M
Virology Research Program (Program 4)P30CA016086 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Deborah F. Tate · 1985 to 2026
$201.5M
UNC-CH CENTER FOR ENVIRONMENTAL HEALTH &SUSCEPTIBILITYP30ES010126 · NIEHS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Melissa A. Troester · 2001 to 2026
$36.3M
Gene Expression Patterns in Human Tumors Identified Using Transcript SequencingU24CA143848 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAYES, DAVID N, PEROU, CHARLES M · 2009 to 2016
$20.8M
Genome Characterization Center (GCC)U24CA143867 · NCI · BROAD INSTITUTE, INC. · PI GABRIEL, STACEY, MEYERSON, MATTHEW L. · 2009 to 2016
$17.0M
The Cancer Genome Atlas Data Analysis CenterU24CA143845 · NCI · BROAD INSTITUTE, INC. · PI CHIN, LYNDA, GETZ, GAD A · 2009 to 2016
$16.0M
Harvard Genome Characterization CenterU24CA144025 · NCI · BRIGHAM AND WOMEN'S HOSPITAL · PI KUCHERLAPATI, RAJU S. · 2009 to 2016
$14.0M
The USC-JHU Cancer Epigenome Characterization CenterU24CA143882 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI BAYLIN, STEPHEN B., WEISENBERGER, DANIEL JOSEPH · 2009 to 2016
$13.3M
MSKCC Center for Translational Cancer Genomic AnalysisU24CA143840 · NCI · SLOAN-KETTERING INST CAN RESEARCH · PI LADANYI, MARC, SANDER, CHRIS · 2009 to 2016
$11.5M
NCI NIH HHS P30 CA016086NCI NIH HHS P30 CA016672NCI NIH HHS R01 CA163722NCI NIH HHS U24 CA143799NCI NIH HHS U24 CA143835NCI NIH HHS U24 CA143840NCI NIH HHS U24 CA143843NCI NIH HHS U24 CA143845NCI NIH HHS U24 CA143848NCI NIH HHS U24 CA143858NCI NIH HHS U24 CA143866NCI NIH HHS U24 CA143867NCI NIH HHS U24 CA143882NCI NIH HHS U24 CA143883NCI NIH HHS U24 CA144025NCI NIH HHS U24 CA210949NCI NIH HHS U24 CA210950NCI NIH HHS U24 CA210957NCI NIH HHS U24 CA210988NCI NIH HHS U24 CA210990NHGRI NIH HHS U54 HG003067NHGRI NIH HHS U54 HG003079NHGRI NIH HHS U54 HG003273NIEHS NIH HHS P30 ES010126
6 · The paper itself

Abstract

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale.

Indexed as

Databases, GeneticGenomicsHumansKaplan-Meier EstimateNeoplasmsProportional Hazards Modelsclinical data resourceCox proportional hazards regression modeldisease-free intervaldisease-specific survivalfollow-up timeoverall survivalprogression-free intervalTCGAThe Cancer Genome Atlastranslational research

Identifiers

PMID29625055
PMCPMC6066282

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

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.