N3C Clinical Cancer Enclave

Overview

The National Clinical Cohort Collaborative (N3C) Cancer Enclave is part of a broader feasibility testing initiative being done to refine the overall governance, data linkage, and institutional partnership components of N3C. The objective of the Cancer Enclave is to test the feasibility of linking data from multiple sources to generate a comprehensive data enclave.

The N3C Cancer Data Enclave will be a centralized, secure, national clinical data resource with powerful analytics capabilities that the research community can use to study Cancer. The focus will be to use real-world clinical data to study differences in cancer patient outcomes and treatment practices.

The overarching goal of this project, which is supported by the Office of the Assistant Secretary for Planning and Evaluation, is to build and strengthen data infrastructure for patient-centered outcomes research (PCOR) in cancer by developing and evaluating linked, longitudinal data that captures the full trajectory of cancer patients’ care and that can be used by researchers to ascertain the impacts of treatments, and treatment variations, on patient outcomes.

Under this objective, NCI will work with NCATS to obtain EHR data from data warehouses from clinical data partners of N3C that have been linked to the data from the corresponding SEER cancer registries or from state cancer registries. The linkage will be done by using privacy-preserving record linkage (PPRL). The linked data will be combined into one cancer database called the N3C Cancer Enclave. The data from the N3C cancer enclave will not be made available to the broader research community at this stage; it will undergo further development and evaluation prior to be being made available to researchers, consistent with the data access policy.

Background

The cancer tenant is part of NCATS Phase II pilots testing the feasibility of extending N3C COVID to other Clinical Domains. The domain specific enclaves have many similarities to N3C COVID, data contributors sign a set of agreements with NCATS (See attached Data Transfer Agreement, Data Use Agreement, and Linkage Honest Broker agreement) which allows the transfer of a limited dataset and linkages with other data such as SEER. The Cancer Enclave, like N3C COVID, is a centralized enclave hosted by NCATS on an AWS Gov Cloud FEDRAMP moderate server for collaborative analytics within Palantir Foundry.

ICS' Role

This N3C Cancer Enclave project utilizes previous work done by Dr. Wilcox and others for the PPRL and the N3C Covid projects. NCI is the overall and scientific lead of the Cancer Enclave. NCATS role is infrastructure, technical implementation, linkage and contracting. Funding is done using a contract mechanism between Washington University and NCATS. NCI provided funds to WashU.

ICS main objectives:

1. Establish a linkage (we have already done this work in the previous PPRL project) of the Missouri state cancer registry data with all patients in its EHR system available using PPRL and validated by checking the accuracy of the PPRL linkage against its internal data.
2. Transfer the linked datasets after IRB approval and completing the DUA between NIH and Washington University.
3. Quarterly submission of the updated EHR data on the linked patients until the end of FY2025.

We receive monthly incidence reports that are in the NAACCR format. We get the longitudinal data through BJC. What we submit must contain the NAACCR item #s. Only linked matches will be submitted.

Contacts

Internal

External

Project Management

Major Tasks & Initiatives

• Azure DevOps Platform Engineering Feature : 45951 : N3C Cancer Enclave

• DW N3C Cancer Enclave Data Discovery User Story 49925

• Request to rely on Johns Hopkins University (JHU) RTR IRB Submitted 10/24/2024

  • N3C Clinical work (including data transfer for the cancer enclave) will happen under a reliance agreement with Hopkins on the N3C Clinical IRB

• Data Use Agreement (DUA) - complete.

• Submit data in OMOP or PCORNet. Once our IRB/DTA/LHB paperwork is complete, they will send project plan, PHI to exclude, and example file.

Task 1.1. Establish linkage of registry and EHR data

Washington University will establish a linkage of the Missouri state cancer registry data with all patients in its EHR system available at the start of the project.  The linkage will be done using PPRL and validated by checking the accuracy of the PPRL linkage against its internal data.

Task 1.2. Establish Data Use Agreement (DUA).

Washington University will establish a DUA with NCATS/NIH to transfer two linked datasets – the deidentified and the synthetic dataset – to N3C. Washington University will also obtain its IRB permission to deposit the datasets.

Task 1.3. Transfer linked datasets to N3C.

Washington University will transfer the linked datasets after IRB approval and completing the DUA between NIH and Washington University.

Task 1.4. Update EHR data each quarter.

Washington University will send updated EHR data on the linked patients each quarter till the end of FY2025.  These data will be used for evaluating changes in treatments and outcomes of the cancer patients over time.

Important Dates & Notes

(As of February 2025)

##Grant period: May 15, 2024 thru May 15, 2026

Deliverables

1. Two (synthetic and deidentified) linked cancer registry-EHR datasets DW
   Identify cohort: create linkage tokens for patients with phenotypes found in the GitHub repository and extract the MCR data in NAACCR format. Due 4/24/2025
2. EHR data updates quarterly DW

Standard Meetings

Currently internal ad-hoc meetings and PI only meetings with Cancer Enclave.

Administrative Details

Tracking Time

Please ensure all work involving the Cancer Enclave is categorized underneath the
N3C Clinical Cancer Enclave project in Tracking Time..
Tentative sourcing but may end up as hourly billing.
Yr 1 Nicole 5%, Snehil 2%, John 2%
Yr 2 Nicole 3%, Snehil 1%, John 1%

IRB

N3C National Clinical Cohort Collaborative IRB ID: # 202410187
N3C DTA IRB ID: # 202501005 (This was the original N3C Covid IRB and name was transferred from Randi Foraker to Adam Wilcox.)
Both of these rely on the John Hopkins IRB.

Digital Landmarks

Project Web Pages

• National Clinical Cohort Collaborative (N3C) (ncats.nih.gov page)
• Pilot Enclaves Overview
• NCI Surveillance, Epidemology, and End Results (SEER) Program
• SEER Linked Databases
• cancer.clinicalcohort.org

Other References

• Extending the OMOP Common Data Model and Standardized Vocabularies to Support Observational Cancer Research

Document Repositories

• Cancer Enclave Documents on WUSTL Box
• Cancer Regroup Meeting slides Nov 2024

Code Repositories

• Instructions and helper files for compiling and submitting your NAACCR data can be found here.
• Detailed documentation for submission can be found here
• Repository for N3C Clinical can be found here

Glossary / Acronyms

Miscellaneous