Computer tools to read and understand DNA from individual cells
Development and Application of Computational Methods for Single Cell DNA Sequencing Data
This project builds new computer methods to analyze DNA from single cells to help researchers spot mutations in cancers and brain conditions.
Quick facts
| Grant type | R01 grant |
|---|---|
| Study type | NIH-funded research |
| Funding institution | Harvard Medical School NIH-funded |
| Lab location | 1 site (Boston, United States) |
| Project ID | NIH-11131162 on NIH RePORTER |
What this research studies
Researchers will create software to analyze whole-genome data generated from single cells and to handle errors that come from DNA amplification. They will develop methods to detect small changes (single-letter mutations and indels) as well as larger changes (copy number and structural variants and tandem repeats). The team will use machine learning approaches, including graph-based models and autoencoder deep learning, and then apply these tools to real questions like genome-editing off-target effects, lineage tracing, and linking driver mutations with copy number changes in brain tumors. The methods will be validated on single-cell datasets from neurons and tumor samples to improve accuracy for future studies.
Who could benefit from this research
Good fit: Ideal candidates would be people with cancers—particularly brain tumors—or others willing to donate tumor tissue, surgical specimens, or blood for single-cell DNA sequencing.
Not a fit: People without conditions driven by somatic mutations or those unable or unwilling to provide tissue or sequencing samples are unlikely to benefit directly from this project.
Why it matters
Potential benefit: If successful, these tools could make it easier to find rare tumor mutations, track how cancers evolve, and support more precise diagnoses and personalized treatments.
How similar studies have performed: Some prior single-cell DNA analyses have produced promising results, but the field still faces technical hurdles and this project aims to address those gaps.
Where this research is happening
Boston, United States
- Harvard Medical School — Boston, United States (Active)
Researchers
- Principal investigator: Park, Peter J — Harvard Medical School
- Study coordinator: Park, Peter J
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.