# Towards Robust Multiplex Genome Engineering Beyond CRISPR-Cas9

> **NIH NIH R35** · STANFORD UNIVERSITY · 2020 · $473,100

## Abstract

Project Abstract
Towards Robust Multiplex Genome Engineering Beyond CRISPR-Cas9
Exemplified by the CRISPR-Cas9 system, gene-editing technology is a powerful collection of
tools for probing the hidden mechanisms of human diseases by understanding and controlling
the functions of human genome variants. However, existing CRISPR genome technologies have
three major limitations: (1) low efficiency and lack of accuracy when making large genome
modifications such as structural variants in complex diseases; (2) uncontrollable off-target
effects that lead to unwanted editing and cellular toxicity; (3) variable activity and precision when
performing CRISPR editing in mammalian genome across different contexts, e.g. genomic loci,
cell types, and model systems. To overcome these limitations, many groups including our own
have sought to develop improved CRISPR tools using experimental methods and computational
techniques. Building on my previous expertise, I will work towards multiplex, robust and error-
free genome engineering. My group will seek to design new microbial proteins with sequence-
independent recombination and RNA-to-DNA editing capabilities (Focus 1). Then, to provide
robust gene-editing tools for studying single-cell genomics, I propose to leverage versatile
CRISPR designs to enable high-capacity cell barcoding to define genome dynamics at single-
cell resolution (Focus 2). To validate our new tools and as initial demonstration, we will use in
human cancer models, with a focus on studying the cellular dynamics that lead to tumor drug
resistance through genetic perturbation (Focus 3). The ultimate goal of my lab is to enable error-
free engineering of genomic variants at any sizes, with robust activities across in vitro and in
vivo applications. I will use this precise toolkit to uncover the functions of long genome
alterations in human diseases, a major “black box” in our genome. The success of the proposal
has the promise to generate safe, reliable genome correction tools for therapeutics.

## Key facts

- **NIH application ID:** 10048673
- **Project number:** 1R35HG011316-01
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** Le Cong
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $473,100
- **Award type:** 1
- **Project period:** 2020-09-01 → 2025-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10048673

## Citation

> US National Institutes of Health, RePORTER application 10048673, Towards Robust Multiplex Genome Engineering Beyond CRISPR-Cas9 (1R35HG011316-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10048673. Licensed CC0.

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