# varCUT&Tag: A Method for Simultaneous Identification and Characterization of Sequence Variants in Regulatory Elements and Genes

> **NIH NIH UG3** · UNIV OF MASSACHUSETTS MED SCH WORCESTER · 2024 · $418,750

## Abstract

PROJECT SUMMARY
Most methods for identification of sequence variants focus either on broad genomic coverage using whole
genome sequencing (WGS), typically at depths of ~50-fold, or higher depth sequencing of coding regions (the
exome) after enrichment using oligonucleotide hybridization strategies. However, typical WGS strategies miss
most rare (< 5%) sequence variants, while WGS at depths required to identify rare variants can be cost-
prohibitive. Exome sequencing approaches can provide high coverage of coding regions at reasonable cost
but miss the vast majority of mutations that occur outside of coding regions. Besides coding regions, genetic
variation in cis regulatory regions (CREs) can have a major impact on cell and tissue function by altering
expression of critical genes. No general enrichment strategies for high depth CRE sequencing have been
described because different regions of the genome act as CREs in different cell types, necessitating different
sequences to be enriched in each cell lineage. Drawing on the fact that CREs are marked by the same set of
epigenetic marks in different cell types, we will leverage recent epigenetic profiling technologies we created to
develop a new method called varCUT&Tag for high coverage sequencing and identification of rare variants
within CREs and gene bodies (UG3 phase). A critical feature of our approach will be the simultaneous
identification of epigenetic marks surrounding each variant, enabling functional characterization of the effects
of somatic mutations on CRE function. We will also develop a single cell version of this approach, which
includes a single cell RNA sequencing component, allowing the effects of sequence variants on gene
expression to be identified. As a result, we will be able to not only identify rare CRE variants in diverse cell and
tissue types, but we will simultaneously prioritize variants that alter CRE function for future studies. Using this
approach, we will work within the SMaHT network to identify and characterize CRE variants from numerous
human tissues, uncover the effects of variants on tissue heterogeneity and cell lineage (using scVarCUT&Tag),
and engage in collaborative studies within the Network to increase variant discovery (all UH3 phase). In sum,
varCUT&Tag will fill a major gap in our understanding of somatic sequence variants and provide mechanistic
insight into their effects in diverse human tissues.

## Key facts

- **NIH application ID:** 10816595
- **Project number:** 5UG3NS132136-02
- **Recipient organization:** UNIV OF MASSACHUSETTS MED SCH WORCESTER
- **Principal Investigator:** Thomas G Fazzio
- **Activity code:** UG3 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $418,750
- **Award type:** 5
- **Project period:** 2023-04-01 → 2025-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10816595

## Citation

> US National Institutes of Health, RePORTER application 10816595, varCUT&Tag: A Method for Simultaneous Identification and Characterization of Sequence Variants in Regulatory Elements and Genes (5UG3NS132136-02). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10816595. Licensed CC0.

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