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. 2018 Apr 5;173(2):400-416.e11.
doi: 10.1016/j.cell.2018.02.052.

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

Jianfang Liu  1 , Tara Lichtenberg  2 , Katherine A Hoadley  3 , Laila M Poisson  4 , Alexander J Lazar  5 , Andrew D Cherniack  6 , Albert J Kovatich  7 , Christopher C Benz  8 , Douglas A Levine  9 , Adrian V Lee  10 , Larsson Omberg  11 , Denise M Wolf  12 , Craig D Shriver  13 , Vesteinn Thorsson  14 ; Cancer Genome Atlas Research Network; Hai Hu  15
Collaborators, Affiliations

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

V体育官网入口 - Jianfang Liu et al. Cell. .

Abstract (V体育2025版)

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 VSports手机版. 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. .

Keywords: Cox proportional hazards regression model; TCGA; The Cancer Genome Atlas; clinical data resource; disease-free interval; disease-specific survival; follow-up time; overall survival; progression-free interval; translational research V体育安卓版. .

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Conflict of interest statement

DECLARATION OF INTERESTS

Michael Seiler, Peter G. Smith, Ping Zhu, Silvia Buonamici, and Lihua Yu are employees of H3 Biomedicine, Inc. Parts of this work are the subject of a patent application: WO2017040526 titled “Splice variants associated with neomorphic sf3b1 mutants. ” Shouyoung Peng, Anant A. Agrawal, James Palacino, and Teng Teng are employees of H3 Biomedicine, Inc. Andrew D. Cherniack, Ashton C. Berger, and Galen F. Gao receive research support from Bayer Pharmaceuticals. Gordon B. Mills serves on the External Scientific Review Board of Astrazeneca. Anil Sood is on the Scientific Advisory Board for Kiyatec and is a shareholder in BioPath. Jonathan S. Serody receives funding from Merck, Inc. Kyle R. Covington is an employee of Castle Biosciences, Inc. Preethi H. Gunaratne is founder, CSO, and shareholder of NextmiRNA Therapeutics. Christina Yau is a part-time employee/consultant at NantOmics. Franz X. Schaub is an employee and shareholder of SEngine Precision Medicine, Inc. Carla Grandori is an employee, founder, and shareholder of SEngine Precision Medicine, Inc. Robert N. Eisenman is a member of the Scientific Advisory Boards and shareholder of Shenogen Pharma and Kronos Bio. Daniel J. Weisenberger is a consultant for Zymo Research Corporation. Joshua M. Stuart is the founder of Five3 Genomics and shareholder of NantOmics. Marc T. Goodman receives research support from Merck, Inc. Andrew J. Gentles is a consultant for Cibermed. Charles M. Perou is an equity stock holder, consultant, and Board of Directors member of BioClassifier and GeneCentric Diagnostics and is also listed as an inventor on patent applications on the Breast PAM50 and Lung Cancer Subtyping assays. Matthew Meyerson receives research support from Bayer Pharmaceuticals; is an equity holder in, consultant for, and Scientific Advisory Board chair for OrigiMed; and is an inventor of a patent for EGFR mutation diagnosis in lung cancer, licensed to LabCorp. Eduard Porta-Pardo is an inventor of a patent for domainXplorer. Han Liang is a shareholder and scientific advisor of Precision Scientific and Eagle Nebula. Da Yang is an inventor on a pending patent application describing the use of antisense oligonucleotides against specific lncRNA sequence as diagnostic and therapeutic tools. Yonghong Xiao was an employee and shareholder of TESARO, Inc. Bin Feng is an employee and shareholder of TESARO, Inc. Carter Van Waes received research funding for the study of IAP inhibitor ASTX660 through a Cooperative Agreement between NIDCD, NIH, and Astex Pharmaceuticals. Raunaq Malhotra is an employee and shareholder of Seven Bridges, Inc. Peter W. Laird serves on the Scientific Advisory Board for AnchorDx. Joel Tepper is a consultant at EMD Serono. Kenneth Wang serves on the Advisory Board for Boston Scientific, Microtech, and Olympus. Andrea Califano is a founder, shareholder, and advisory board member of DarwinHealth, Inc. and a shareholder and advisory board member of Tempus, Inc VSports最新版本. Toni K. Choueiri serves as needed on advisory boards for Bristol-Myers Squibb, Merck, and Roche. Lawrence Kwong receives research support from Array BioPharma. Sharon E. Plon is a member of the Scientific Advisory Board for Baylor Genetics Laboratory. Beth Y. Karlan serves on the Advisory Board of Invitae.

Figures

Figure 1
Figure 1. Clinical Data Analysis
(A–E) Flowchart (A) and K-M plots of the Pan-Cancer types for OS (B), PFI (C), DFI (D), and DSS (E) respectively. The tail of each K-M curve is truncated at the point when fewer than 10 patients remain at risk. See Figure S1 for plots of the 4 endpoints within each of the 33 tumor types and Tables S1, S2, S3 and S4 for more detailed information regarding endpoint derivation.
Figure 2
Figure 2. Validation and Application Examples
(A–D) Clinical survival outcomes of breast cancer patients with ER+ or ER− tumors using (A) OS, (B) PFI, (C) DFI, and (D) DSS as the endpoint, respectively. Plots were truncated at 10 years, but the analyses were conducted using all of the data. (E–G) Pairwise plots comparing natural logHRs for event development measured by three different clinical endpoints (OS, DSS, and PFI), with natural logHRs calculated for high-stage (III, IV) disease relative to low-stage (I, II) disease: (E) PFI versus OS, (F) PFI versus DSS, and (G) OS versus DSS. Here 14 diseases for which these three endpoints are recommended for use are analyzed. The blue diagonal lines illustrate equal logHRs measured by each endpoint pair. Error bars represents the standard errors of logHR. Red error bars show models that did not satisfy the PHs assumption.
See this image and copyright information in PMC

"VSports在线直播" References

    1. Altman DG, McShane LM, Sauerbrei W, Taube SE. Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK): explanation and elaboration. PLoS Med. 2012;9:e1001216. - PMC - PubMed
    1. Amin MB, Greene FL, Edge SB, Compton CC, Gershenwald JE, Brookland RK, Meyer L, Gress DM, Byrd DR, Winchester DP. The Eighth Edition AJCC Cancer Staging Manual: Continuing to build a bridge from a population-based to a more “personalized” approach to cancer staging. CA Cancer J Clin. 2017;67:93–99. - PubMed (V体育2025版)
    1. Anderson JR, Cain KC, Gelber RD. Analysis of survival by tumor response. J Clin Oncol. 1983;1:710–719. - PubMed
    1. Anderson JR, Cain KC, Gelber RD. Analysis of survival by tumor response and other comparisons of time-to-event by outcome variables. J Clin Oncol. 2008;26:3913–3915. - "VSports手机版" PubMed
    1. Bachy E, Brice P, Delarue R, Brousse N, Haioun C, Le Gouill S, Delmer A, Bordessoule D, Tilly H, Corront B, et al. Long-term follow-up of patients with newly diagnosed follicular lymphoma in the prerituximab era: effect of response quality on survival–A study from the groupe d’etude des lymphomes de l’adulte. J Clin Oncol. 2010;28:822–829. - PubMed

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