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      NCI Cancer Research Data Commons: Cloud-Based Analytic Resources

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The NCI's Cloud Resources (CR) are the analytical components of the Cancer Research Data Commons (CRDC) ecosystem. This review describes how the three CRs (Broad Institute FireCloud, Institute for Systems Biology Cancer Gateway in the Cloud, and Seven Bridges Cancer Genomics Cloud) provide access and availability to large, cloud-hosted, multimodal cancer datasets, as well as offer tools and workspaces for performing data analysis where the data resides, without download or storage. In addition, users can upload their own data and tools into their workspaces, allowing researchers to create custom analysis workflows and integrate CRDC-hosted data with their own.

          See related articles by Brady et al., p. 1384, Wang et al., p. 1388, and Kim et al., p. 1404

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          Most cited references20

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          The NCI Genomic Data Commons

          Allison P. Heath, Vincent Ferretti, Stuti Agrawal … (2021)
          Article 0 comments Cited 40 times – based on 0 reviews     Review now
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            Radiation-related genomic profile of papillary thyroid cancer after the Chernobyl accident

            Lindsay M Morton, Danielle M Karyadi, Chip Stewart … (2021)
            The 1986 Chernobyl nuclear power plant accident increased papillary thyroid cancer (PTC) incidence in surrounding regions, particularly for 131 I-exposed children. We analyzed genomic, transcriptomic, and epigenomic characteristics of 440 PTCs from Ukraine (359 with estimated childhood 131 I exposure and 81 unexposed children born after 1986). PTCs displayed radiation dose-dependent enrichment of fusion drivers, nearly all in the mitogen-activated protein kinase pathway, and increases in small deletions and simple/balanced structural variants that were clonal and bore hallmarks of non-homologous end-joining repair. Radiation-related genomic alterations were more pronounced for those younger at exposure. Transcriptomic and epigenomic features were strongly associated with driver events but not radiation dose. Our results point to DNA double-strand breaks as early carcinogenic events that subsequently enable PTC growth following environmental radiation exposure.
            Article 0 comments Cited 35 times – based on 0 reviews     Review now
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              Is Open Access

              AGO-bound mature miRNAs are oligouridylated by TUTs and subsequently degraded by DIS3L2

              Acong Yang, Tie-Juan Shao, Xavier Bofill-De Ros … (2020)
              MicroRNAs (miRNAs) associated with Argonaute proteins (AGOs) regulate gene expression in mammals. miRNA 3’ ends are subject to frequent sequence modifications, which have been proposed to affect miRNA stability. However, the underlying mechanism is not well understood. Here, by genetic and biochemical studies as well as deep sequencing analyses, we find that AGO mutations disrupting miRNA 3’ binding are sufficient to trigger extensive miRNA 3’ modifications in HEK293T cells and in cancer patients. Comparing these modifications in TUT4, TUT7 and DIS3L2 knockout cells, we find that TUT7 is more robust than TUT4 in oligouridylating mature miRNAs, which in turn leads to their degradation by the DIS3L2 exonuclease. Our findings indicate a decay machinery removing AGO-associated miRNAs with an exposed 3’ end. A set of endogenous miRNAs including miR-7, miR-222 and miR-769 are targeted by this machinery presumably due to target-directed miRNA degradation.
              Article 0 comments Cited 33 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Cancer Res
                Journal ID (iso-abbrev): Cancer Res
                Title: Cancer Research
                Publisher: American Association for Cancer Research
                ISSN (Print): 0008-5472
                ISSN (Electronic): 1538-7445
                Publication date (Print): 02 May 2024
                Publication date (Electronic): 15 March 2024
                Volume: 84
                Issue: 9
                Pages: 1396-1403
                Affiliations
                [1 ]General Dynamics Information Technology, Falls Church, Virginia.
                [2 ]Velsera (Seven Bridges), Charlestown, Massachusetts.
                [3 ]Broad Institute, Cambridge, Massachusetts.
                [4 ]Frederick National Laboratory for Cancer Research, Frederick, Maryland.
                [5 ]Center for Biomedical Informatics and Information Technology, NCI, Rockville, Maryland.
                [6 ]Trans Divisional Research Program, Division of Cancer Epidemiology and Genetics, NCI, Rockville, Maryland.
                Author notes
                [#]

                D. Pot, Z. Worman, and A. Baumann contributed equally to this article.

                [* ] Corresponding Author: Erin Beck, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850. E-mail: erin.beck2@ 123456nih.gov

                Cancer Res 2024;84:1396–403

                Author information
                https://orcid.org/0000-0002-1480-9826
                https://orcid.org/0000-0002-7619-7466
                https://orcid.org/0000-0001-7899-3389
                https://orcid.org/0009-0000-4046-3710
                https://orcid.org/0000-0003-2826-940X
                https://orcid.org/0000-0002-0848-5853
                https://orcid.org/0009-0006-5102-3116
                https://orcid.org/0000-0001-8799-9029
                https://orcid.org/0000-0001-7811-8613
                https://orcid.org/0009-0007-7018-916X
                https://orcid.org/0000-0002-5471-3300
                https://orcid.org/0000-0001-6190-9304
                https://orcid.org/0000-0002-3954-9653
                Article
                Publisher ID: CAN-23-2657
                DOI: 10.1158/0008-5472.CAN-23-2657
                PMC ID: 11063685
                PubMed ID: 38488504
                SO-VID: 38d24ac3-f4f5-404c-91e3-163e8e5139e0
                Copyright © ©2024 The Authors; Published by the American Association for Cancer Research
                License:

                This open access article is distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) license.

                History
                Date received : 09 September 2023
                Date revision received : 26 January 2024
                Date accepted : 05 March 2024
                Page count
                Pages: 8
                Funding
                Funded by: Center for Biomedical Informatics and Information Technology (CBIIT), DOI 10.13039/100020082;
                Award ID: 75N91019D00024
                Award Recipient :
                Funded by: Center for Biomedical Informatics and Information Technology (CBIIT), DOI 10.13039/100020082;
                Award ID: HHSN261201400008C
                Award Recipient :
                Funded by: Center for Biomedical Informatics and Information Technology (CBIIT), DOI 10.13039/100020082;
                Award ID: HHSN261201500003I
                Award Recipient :
                Categories
                Subject: Computational Methods
                Subject: Computational Methods
                Subject: Database Resources
                Subject: Imaging
                Subject: Reviews

                Data availability:

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