Publications

Over the last 10 years, CRDC data and resources have served as the foundation for an extensive body of cancer research. CRDC’s impact is evident through more than 48,000 data citations as documented by PubMed and Google Scholar. Additionally, hundreds of publications have referenced papers authored by the CRDC team.

The CRDC tracks peer-reviewed papers that include:

• Data from major NCI-funded research programs (e.g., TCGA, CPTAC)
• Re-used CRDC data for validation, comparative analysis, and/or to test computational methods
• The use of analytical tools accessible through CRDC Data Commons or the NCI Cloud Resource

The following papers illustrate the use of CRDC data and resources. Below are abbreviated versions of each paper's PubMed abstract.  

Integrative Analysis of Lung Adenocarcinoma Across Diverse Ethnicities and Exposures  _{— Cancer Cell}

This comprehensive proteogenomic analysis of LUAD tumors and matched normal adjacent tissues from 406 patients across diverse geographic and demographic backgrounds explores the impact of understudied driver mutations, prognostic role of chromosomal instability, patterns of immune signaling, differential and sex-specific effects of endogenous mutagens and environmental carcinogens, and pathobiology of early-stage tumors with "late-like" characteristics. Candidate protein biomarkers are proposed for unstable tumors with highly fragmented genomes and for carcinogen exposures, and a LUAD subtype-specific atlas of therapeutic vulnerabilities is presented. 

Researchers used multiple datasets, including several shared through the Proteomic Data Commons. Find their list of datasets. 

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Three-Dimensional Genome Landscape of Primary Human Cancers  _{— Nature Genetics}

Integrative analyses revealed the enhancer landscape of noncancer cells in the tumor microenvironment for genes related to immune escape. Deep whole-genome sequencing and enhancer connectome mapping provided accurate detection and validation of diverse structural variants across cancer genomes and revealed distinct enhancer rewiring consequences from noncoding point mutations, genomic inversions, translocations and focal amplifications. Extrachromosomal DNA promoted more extensive enhancer rewiring among several types of focal amplification mechanisms. 

Researchers referenced data from The Cancer Genome Atlas available through the Genomic Data Commons. Find their list of datasets.

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Oncopacket: Integration of Cancer Research Data Using GA4GH Phenopackets _{— Bioinformatics}

Lack of data integration remains a significant impediment to cancer research, and many analyses still require customized software to transform and prepare cancer data. We describe a software package to harmonize genetic and clinical cancer data into the GA4GH Phenopacket schema, an ISO standard for representing clinical case data. We integrated demographic, mutation, morphology, diagnosis, intervention, and survival data using case data from the National Cancer Institute for 12 cancer types. The Phenopacket standard provides a foundation for downstream use, including sophisticated statistical and AI/ML analyses. 

Researchers used multiple datasets from across the CRDC. Find their description of datasets.   

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Barking Up the Right Tree: RNA-seq Data for Immune Checkpoint Study in Humans and Dogs _{— PLOS Computational Biology}  

Here, we examine the RNA-seq-based expression of 44 ICs across 14 canine cancer types and an extensive human dataset. We unveil diverse canine IC expression patterns and unique human IC signatures that reflect the histological type and primary site of cancer. We uncover a striking similarity between canine brain cancers, osteosarcoma, and their human counterparts, identifying them as prospective immunotherapy models. Four ICs - CD160, A2AR, NKG2A, and OX40 - are key to the differences observed between species. We also find that individual human IC signatures vary in how well they align with their respective cancer types, a pattern that may influence future approaches to personalized therapy. 

Researchers used multiple datasets from the Integrated Canine Data Commons.

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Explore the foundational CRDC publications that describe the systems, data standards, cloud-based platforms, and specialized data commons that help researchers around the world work with NCI-funded cancer research data.     

Reference Publications  Find publications about CRDC's data commons and resources. 

Explore the collection of peer-reviewed publications that showcase the breadth and depth of research using CRDC data and resources. This includes publications from across the CRDC Data Commons and Cloud Resource that illustrate how CRDC data, tools, and resources are used by the research community.  

Select Publications  Find a list of peer-reviewed publications. 

NCI Cancer Research Data Commons (CRDC) should be cited with the URL "datacommons.cancer.gov" and the following paper:


Kim E, Davidsen T, Davis-Dusenbery BN, Baumann A, Maggio A, Chen Z, Meerzaman D, Casas-Silva E, Pot D, Pihl T, Otridge J, Shalley E; CRDC Program; Barnholtz-Sloan JS, Kerlavage AR. NCI Cancer Research Data Commons: Lessons Learned and Future State. Cancer Res. 2024 May 2;84(9):1404-1409. doi: 10.1158/0008-5472.CAN-23-2730. PMID: 38488510; PMCID: PMC11063686.

When citing individual data commons or the CRDC cloud resource, please refer to the attribution policies of those CRDC components, available on their microsites and portals.