# Simultaneous mapping of somatic mosaicism and kb-resolution 3D genome in single cells.

> **NIH NIH UG3** · CASE WESTERN RESERVE UNIVERSITY · 2024 · $402,500

## Abstract

Project Abstract
In early development and over the lifetime of a human, the genome of every somatic cell will eventually
accumulate hundreds of mutations during multiple cell divisions. Although most somatic mutations are
predicted to be non-functional, it is known for a long time that some of the somatic mutations, including
single nucleotide variants (SNVs), copy number variants (CNVs), translocations, etc., may cause serious
diseases like cancer. In the past decade, more and more studies suggested that somatic mutations may
also play important roles in milder complex diseases, such as autism. However, although single-cell or
ultra-deep whole genome sequencing (WGS) technologies can now identify many rare somatic mutations,
these technologies tell little about the consequences or mechanisms of somatic mutations. In fact, unless
a somatic mutation causes significant clonal expansion, characterizing the molecular functions of a
somatic mutation in its native tissue context is extremely challenging. In general, WGS protocol precludes
most of the commonly pursued epigenomic technologies such as ATAC-seq and ChIP-seq. We recent
demonstrated that using a novel deep-learning-based pipeline named DeepLoop, we can upgrade the
super sparse single cell Hi-C maps to kilobase resolution, which may serve as a robust readout of
genome activity. This motivates us to optimize a technology named Dip-C to simultaneously map somatic
mutations and 3D genome from single cells. If successful, the project will deliver a long needed multi-
OMIC tool for SMaHT network. We will test Dip-C in both model cell line and human tissues and verify
its unique capability to resolve how somatic mutations may affect a small number of cells in large
population or complex tissue.

## Key facts

- **NIH application ID:** 10827510
- **Project number:** 5UG3NS132061-02
- **Recipient organization:** CASE WESTERN RESERVE UNIVERSITY
- **Principal Investigator:** Fulai Jin
- **Activity code:** UG3 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $402,500
- **Award type:** 5
- **Project period:** 2023-04-15 → 2025-09-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10827510

## Citation

> US National Institutes of Health, RePORTER application 10827510, Simultaneous mapping of somatic mosaicism and kb-resolution 3D genome in single cells. (5UG3NS132061-02). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10827510. Licensed CC0.

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