inst/markdown/resources.markdown

In CRI-iAtlas/iatlas-app: What the Package Does (One Line, Title Case)

Updates

Follow @iatlas_cri on Twitter for latest developments!

Source code and data resources

iAtlas app, tools, and data and annotations

• GitHub: https://github.com/CRI-iAtlas
• GitLab: https://gitlab.com/cri-iatlas
• iAtlas Notebooks: https://github.com/CRI-iAtlas/iatlas-notebooks
• Synapse: https://www.synapse.org/#!Synapse:syn10337516/wiki/458420
• Immune Subtype Classifier: https://github.com/CRI-iAtlas/ImmuneSubtypeClassifier
• DockStore: https://dockstore.org/organizations/SageBionetworks/collections/iatlas

TCGA originating sources

• TCGA PanCancer Atlas: https://gdc.cancer.gov/about-data/publications/pancanatlas
• Immune Landscape of Cancer Manuscript Page: https://gdc.cancer.gov/about-data/publications/panimmune
• The Cancer Genome Atlas: http://cancergenome.nih.gov/
• NCI Genomic Data Commons: https://portal.gdc.cancer.gov/

Source for targets of immunotherapy studies

• CRI Landscape of Immuno-Oncology Drug Development: https://www.cancerresearch.org/scientists/immuno-oncology-landscape

Source for data in the Molecular Response to Immune Checkpoint Inhibitor modules:

• Choueiri et al. Immunomodulatory Activity of Nivolumab in Metastatic Renal Cell Carcinoma. Clin Cancer Res. 2016;22(22):5461-5471

• Cloughesy et al. Neoadjuvant anti-PD-1 immunotherapy promotes a survival benefit with intratumoral and systemic immune responses in recurrent glioblastoma. Nat Med. 2019 Mar;25(3):477-486

• [Gide et al. Distinct Immune Cell Populations Define Response to Anti-PD-1 Monotherapy and Anti-PD-1/Anti-CTLA-4 Combined Therapy. Cancer Cell. 2019 Feb 11;35(2):238-255.e6](https://www.cell.com/cancer-cell/fulltext/S1535-6108(19)30037-6)

• [Hugo et al. Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma. Cell. 2016 Mar 24;165(1):35-44](https://www.cell.com/cell/fulltext/S0092-8674(16)30215-X)

• Kim et al. Comprehensive molecular characterization of clinical responses to PD-1 inhibition in metastatic gastric cancer. Nat Med. 2018 Sep;24(9):1449-1458. doi: 10.1038/s41591-018-0101-z. Epub 2018 Jul 16. PMID: 30013197

• Liu et al. Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma [published correction appears in Nat Med. 2020 Jul;26(7):1147]. Nat Med. 2019;25(12):1916-1927

• Mariathasan et al. TGFβ attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells. Nature. 2018 Feb 22;554(7693):544-548

• McDermott et al. Clinical activity and molecular correlates of response to atezolizumab alone or in combination with bevacizumab versus sunitinib in renal cell carcinoma. Nat Med. 2018 Dec;24(12):1941. Nat Med. 2018;24(6):749-757

• Miao et al. Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science. 2018;359(6377):801-806

• [Riaz et al. Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab. Cell. 2017 Nov 2;171(4):934-949.e16](https://www.cell.com/cell/fulltext/S0092-8674(17)31122-4)

• Van Allen et al. Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science. 2015 Oct 9;350(6257):207-211

• Zhao et al. Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma [published correction appears in Nat Med. 2019 Apr 17;:]. Nat Med. 2019;25(3):462-469

Workflows

Workflows for characterization of immune environment in cancer

• CWL workflows: https://github.com/CRI-iAtlas/iatlas-workflows
• Docker tools: https://quay.io/organization/cri-iatlas

Manuscripts

• Eddy et al. CRI iAtlas: an interactive portal for immuno-oncology research. F1000Research 2020, 9:1028

• Gibbs DL, Robust classification of Immune Subtypes in Cancer, bioRxiv 2020.01.17.910950

• [Saltz et al. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell Rep. 2018 Apr 3;23(1):181-193.e7](https://www.cell.com/cell-reports/fulltext/S2211-1247(18)30447-9)

• [Sayaman et al. Germline genetic contribution to the immune landscape of cancer. Immunity. 2021 Feb 9;54(2):367-386.e8](https://www.cell.com/immunity/fulltext/S1074-7613(21)00034-0)

• [Thorsson et al. The Immune Landscape of Cancer. Immunity. 2018 Apr 17;48(4):812-830.e14](https://www.cell.com/immunity/fulltext/S1074-7613(18)30121-3)

• Upadhaya et al. Immuno-oncology drug development forges on despite COVID-19. Nat Rev Drug Discov. 2020 Nov;19(11):751-752

Organizations

Organizations contributing to CRI iAtlas

• Cancer Research Institute: http://cancerresearch.org
• Sage Bionetworks: http://www.sagebionetworks.org
• Institute for Systems Biology: http://www.isbscience.org
• UNC Lineberger Comprehensive Cancer Center: https://unclineberger.org

CRI-iAtlas/iatlas-app documentation built on Feb. 7, 2025, 9:02 p.m.