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
• Synapse: https://www.synapse.org/#!Synapse:syn10337516/wiki/458420
• Immune Subtype Classifier: https://github.com/CRI-iAtlas/ImmuneSubtypeClassifier

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:

• 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

• 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

• 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

• Riaz et al. Tumor and Microenvironment Evolution during Immunotherapy with Nivolumab. Cell. 2017 Nov 2;171(4):934-949.e16

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

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

• Sayaman et al. Germline genetic contribution to the immune landscape of cancer. Immunity. 2021 Feb 9;54(2):367-386.e8

• Thorsson et al. The Immune Landscape of Cancer. Immunity. 2018 Apr 17;48(4):812-830.e14

• 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 iAtlas

• Sage Bionetworks: https://www.sagebionetworks.org
• Institute for Systems Biology: https://www.isbscience.org
• UNC Lineberger: https://unclineberger.org
• Vincent Lab: https://unclineberger.org/vincentlab/
• Cancer Research Institute: https://cancerresearch.org/