# Ultra-sensitive, unbiased, high-throughput, biochemical CHANGE-seq genome-wide activity and gRNA sequencing assays for therapeutic genome editing INDs

> **NIH NIH U01** · ST. JUDE CHILDREN'S RESEARCH HOSPITAL · 2024 · $479,100

## Abstract

PROJECT SUMMARY
Genome editors, technologies to modify the genomes of living cells, have extraordinary potential to become
safe and effective genomic medicines, direct treatments for the underlying cause of genetic diseases such as
sickle cell disease and many others. However, as gene therapy products with novel mechanisms of action, there
remains a need for optimized and qualified biochemical IND-enabling assays to assess their safety. We and
others have developed sensitive and unbiased research methods for defining the genome-wide activity of editors
such as CHANGE-seq and GUIDE-seq. However, they require further optimization and characterization as fit-
for-purpose assays to fulfill rigorous regulatory requirements for investigational new drug (IND) submissions.
Surprisingly, to our knowledge there are no published methods for high-throughput sequencing characterization
of gRNA identity and purity. Thus, there remain urgent unmet needs for publicly available, optimized, and
qualified IND-enabling assays to characterize critical genome editing reagents and their associated on- and off-
target genome-wide activities. We, therefore, propose the following specific aims: 1) Optimize and qualify
CHANGE-seq as IND-enabling biochemical genome-wide activity assay, and 2) Optimize and qualify gRNA
sequencing as IND-enabling assay to assess genome editing component identity and purity, and 3) Collaborate
to test CHANGE-seq and gRNA sequencing in therapeutic contexts. We anticipate that fulfilling the need for
well-characterized assays to identify impurities in critical reagents or characterize key quality attributes of
genome editing drug products will have positive impact to accelerate the translation of novel, safe, and effective
therapeutic genome editing therapeutic strategies to first-in-human clinical trials.

## Key facts

- **NIH application ID:** 10843188
- **Project number:** 5U01AI176471-02
- **Recipient organization:** ST. JUDE CHILDREN'S RESEARCH HOSPITAL
- **Principal Investigator:** Shengdar Tsai
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $479,100
- **Award type:** 5
- **Project period:** 2023-05-17 → 2026-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10843188

## Citation

> US National Institutes of Health, RePORTER application 10843188, Ultra-sensitive, unbiased, high-throughput, biochemical CHANGE-seq genome-wide activity and gRNA sequencing assays for therapeutic genome editing INDs (5U01AI176471-02). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10843188. Licensed CC0.

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