ANNOUNCEMENT

NOBEL PRIZE 2026

This year's laureates, their fields, and the discoveries that earned them the prize.Live nowSee the winners
Moonbase
← Back to Awards
NIHNATIONAL CANCER INSTITUTE

Software and algorithms for elucidating the structure, function, and evolution of extrachromosomal DNA

Completed
Institution
UNIVERSITY OF CALIFORNIA, SAN DIEGO, CA
Principal investigator
Vineet Bafna
Funding
$731K
Duration
2021–2026
Open portfolio

Moonbase score

Still being scored

Abstract

Project Summary Somatic copy number amplification (SCNA) of tumor promoting oncogenes, and focal copy number amplifi- cations specifically, are a major driver of cancer pathogenicity. Recent results have revealed that 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 sub-types, but rarely in normal cells. Unresolved questions regarding the formation, evolution, het- erogeneity, 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) de- velop CAPER (a Community Accessible Pipeline for EcDNA Reconstruction) by leveraging the GenePattern ecosystem to provide an easy point and click interface to running the CPU, memory and storage heavy soft- ware; (2) design and implement novel algorithmic improvements to the CAPER work flow, including support for long-reads and integration of Omics data; and, (3) enable the broad adoption of CAPER through strategic collaborations, outreach and education.

Research team

  • Vineet BafnaPI
  • Jill P. MesirovPI

LOADING MOONBASE SCORE

NATIONAL CANCER INSTITUTEU24ZCA1-RTRB-R(M3)pathogenicityecdnaevolutionamplificationfocalcopy numbercopystructure function

Questions for UNIVERSITY OF CALIFORNIA, SAN DIEGO

Answered by the team behind this research.

No questions yet. Sign in to ask the first one

Related grants

Same researchers, same institution, same topic, scored first.