U24CA264379
Cooperative Agreement
Overview
Grant Description
Software and Algorithms for Elucidating the Structure, Function, and Evolution of Extrachromosomal DNA - Project Summary
Somatic copy number amplification (SCNA) of tumor-promoting oncogenes, and focal copy number amplifications specifically, are a major driver of cancer pathogenicity. Recent results have revealed that focal oncogene amplification is mediated to a large extent by extrachromosomal DNA (ECDNA), i.e., large (1.3 MB on average), highly amplified, oncogene-containing circular molecules that occur in nearly 25% of cancers across all subtypes, but rarely in normal cells.
Unresolved questions regarding the formation, evolution, heterogeneity, and pathogenicity of ECDNA are becoming central to uncovering vulnerabilities that can be targeted for diagnostics and therapy. The proposed project will enhance and disseminate "Software and Algorithms for Elucidating the Structure, Function, and Evolution of Extrachromosomal DNA."
Specifically, we will:
1. Develop CAPER (a community-accessible pipeline for ECDNA reconstruction) by leveraging the GenePattern ecosystem to provide an easy point-and-click interface for running the CPU, memory, and storage-heavy software.
2. Design and implement novel algorithmic improvements to the CAPER workflow, including support for long-reads and integration of omics data.
3. Enable the broad adoption of CAPER through strategic collaborations, outreach, and education.
Somatic copy number amplification (SCNA) of tumor-promoting oncogenes, and focal copy number amplifications specifically, are a major driver of cancer pathogenicity. Recent results have revealed that focal oncogene amplification is mediated to a large extent by extrachromosomal DNA (ECDNA), i.e., large (1.3 MB on average), highly amplified, oncogene-containing circular molecules that occur in nearly 25% of cancers across all subtypes, but rarely in normal cells.
Unresolved questions regarding the formation, evolution, heterogeneity, and pathogenicity of ECDNA are becoming central to uncovering vulnerabilities that can be targeted for diagnostics and therapy. The proposed project will enhance and disseminate "Software and Algorithms for Elucidating the Structure, Function, and Evolution of Extrachromosomal DNA."
Specifically, we will:
1. Develop CAPER (a community-accessible pipeline for ECDNA reconstruction) by leveraging the GenePattern ecosystem to provide an easy point-and-click interface for running the CPU, memory, and storage-heavy software.
2. Design and implement novel algorithmic improvements to the CAPER workflow, including support for long-reads and integration of omics data.
3. Enable the broad adoption of CAPER through strategic collaborations, outreach, and education.
Funding Goals
TO PROVIDE FUNDAMENTAL INFORMATION ON THE CAUSE AND NATURE OF CANCER IN PEOPLE, WITH THE EXPECTATION THAT THIS WILL RESULT IN BETTER METHODS OF PREVENTION, DETECTION AND DIAGNOSIS, AND TREATMENT OF NEOPLASTIC DISEASES. CANCER BIOLOGY RESEARCH INCLUDES THE FOLLOWING RESEARCH PROGRAMS: CANCER CELL BIOLOGY, CANCER IMMUNOLOGY, HEMATOLOGY AND ETIOLOGY, DNA AND CHROMOSOMAL ABERRATIONS, TUMOR BIOLOGY AND METASTASIS, AND STRUCTURAL BIOLOGY AND MOLECULAR APPLICATIONS.
Grant Program (CFDA)
Awarding / Funding Agency
Place of Performance
La Jolla,
California
92093
United States
Geographic Scope
Single Zip Code
Related Opportunity
Analysis Notes
Amendment Since initial award the total obligations have increased 366% from $749,120 to $3,494,584.
San Diego University Of California was awarded
ECDNA Software & Algorithms: Structure, Function, Evolution
Cooperative Agreement U24CA264379
worth $3,494,584
from National Cancer Institute in September 2021 with work to be completed primarily in La Jolla California United States.
The grant
has a duration of 5 years and
was awarded through assistance program 93.396 Cancer Biology Research.
The Cooperative Agreement was awarded through grant opportunity Advanced Development of Informatics Technologies for Cancer Research and Management (U24 Clinical Trial Optional).
Status
(Ongoing)
Last Modified 9/5/25
Period of Performance
9/1/21
Start Date
8/31/26
End Date
Funding Split
$3.5M
Federal Obligation
$0.0
Non-Federal Obligation
$3.5M
Total Obligated
Activity Timeline
Subgrant Awards
Disclosed subgrants for U24CA264379
Transaction History
Modifications to U24CA264379
Additional Detail
Award ID FAIN
U24CA264379
SAI Number
U24CA264379-2576413226
Award ID URI
SAI UNAVAILABLE
Awardee Classifications
Public/State Controlled Institution Of Higher Education
Awarding Office
75NC00 NIH National Cancer Institute
Funding Office
75NC00 NIH National Cancer Institute
Awardee UEI
UYTTZT6G9DT1
Awardee CAGE
50854
Performance District
CA-50
Senators
Dianne Feinstein
Alejandro Padilla
Alejandro Padilla
Budget Funding
| Federal Account | Budget Subfunction | Object Class | Total | Percentage |
|---|---|---|---|---|
| National Cancer Institute, National Institutes of Health, Health and Human Services (075-0849) | Health research and training | Grants, subsidies, and contributions (41.0) | $1,339,646 | 100% |
Modified: 9/5/25