# Comprehensive and Robust Tools for Analysis of Tumor Heterogeneity and Evolution

> **NIH NIH U24** · PRINCETON UNIVERSITY · 2022 · $81,000

## Abstract

This is a collaborative project between Dr. Fei Chen’s IMAT project (R33CA246455) and Dr. Ben
Raphael’s ITCR project (U24CA248453). In this project, we will develop an integrated
experimental and computational platform to analyze the spatial organization of clones in tumor
samples. This platform will combine the Slide-RNA-SeqV2 and Slide-DNA-seq technologies
under development in PI Chen’s IMAT project with customized computational algorithms that
extend the work in PI Raphael’s ITCR project. The proposed work is organized in two aims. In
the first aim, we will extend and optimize computational tools under development in the ITCR
project to identify allele-specific copy number aberrations and spatial distribution of tumor
clones in Slide-RNA-SeqV2 data generated the IMAT project. In the second aim, PI Chen will
generate high resolution spatial DNA data using Slide-seq. This data will uniquely integrate with
computational algorithms from the Raphael group who showed that using allele-specific copy
number aberrations led to much more reliable reconstructions of tumor evolution than total
copy numbers in 10X Genomics whole-genome single-cell sequencing data. The combination of
Slide-RNA-seq data, Slide-DNA-seq data and advanced computational approaches will enable
novel studies of the spatial distribution of clones within tumors and the spatiotemporal
patterns of tumor evolution.

## Key facts

- **NIH application ID:** 10677268
- **Project number:** 3U24CA248453-03S1
- **Recipient organization:** PRINCETON UNIVERSITY
- **Principal Investigator:** Benjamin Raphael
- **Activity code:** U24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $81,000
- **Award type:** 3
- **Project period:** 2020-09-24 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10677268

## Citation

> US National Institutes of Health, RePORTER application 10677268, Comprehensive and Robust Tools for Analysis of Tumor Heterogeneity and Evolution (3U24CA248453-03S1). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10677268. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*