Analyzing large DNA changes in cancer with long-read sequencing
Center for the Comprehensive Analysis of Cancer Somatic Copy-Number Alterations, Rearrangements, and Long-Read Sequencing Data
['FUNDING_OTHER'] · BROAD INSTITUTE, INC. · NIH-11190857
This program builds tools to read and map big DNA changes and rearrangements in tumors to improve understanding and care for people with cancer.
Quick facts
| Phase | ['FUNDING_OTHER'] |
|---|---|
| Study type | Nih_funding |
| Sex | All |
| Sponsor | BROAD INSTITUTE, INC. (nih funded) |
| Locations | 1 site (CAMBRIDGE, UNITED STATES) |
| Trial ID | NIH-11190857 on ClinicalTrials.gov |
What this research studies
From a patient's perspective, this center develops and applies computer tools to find large DNA gains, losses, and rearrangements in tumor genomes using both standard short-read and newer long- or linked-read sequencing. The team combines copy-number calls with parental haplotypes and ancestry information to improve how precisely tumor DNA changes are located. They reconstruct each tumor's genome and its evolutionary history, including tumor purity, ploidy, and subclonal changes, and use those reconstructions to infer DNA damage and repair events. The work builds on prior large efforts like TCGA and PCAWG and aims to make these methods available to researchers and clinical partners.
Who could benefit from this research
Good fit: Ideal candidates are people with cancer whose tumors have been or could be sequenced and who are willing to have their genomic data used for research or shared with collaborating labs.
Not a fit: Patients without cancer or those whose care does not include tumor genomic testing are unlikely to receive direct benefit from this project.
Why it matters
Potential benefit: If successful, this work could produce more accurate genomic maps of tumors that help improve diagnosis and guide more precise treatment choices.
How similar studies have performed: Similar approaches have proven useful before—the team led SCNA analyses for TCGA and co-led PCAWG structural-variation work—so this effort builds on established successes.
Where this research is happening
CAMBRIDGE, UNITED STATES
- BROAD INSTITUTE, INC. — CAMBRIDGE, UNITED STATES (ACTIVE)
Researchers
- Principal investigator: BEROUKHIM, RAMEEN — BROAD INSTITUTE, INC.
- Study coordinator: BEROUKHIM, RAMEEN
About this research
- This is an active NIH-funded research project — typically early-stage science, not a clinical trial accepting patient enrollment.
- Some NIH-funded labs run parallel clinical studies or seek volunteers for related work. To check, contact the principal investigator or institution listed above.
- For full project details, budget, and progress reports, visit the official NIH RePORTER page below.
Conditions: Cancer Diagnostics, Cancers