# Center for Mouse Genomic Variation at Single Cell Resolution

> **NIH NIH UM1** · UNIVERSITY OF CALIFORNIA-IRVINE · 2022 · $2,534,261

## Abstract

Any human being has on average 5 million single-nucleotide variants and 13 million
nucleotides of insertions, deletions, and other regions present in variable copy numbers
compared to the human reference genome. Together these variants must account for all of the
genetic contributions to every phenotype of that person, whether it is their height or their familial
predisposition to complex diseases. While we can quickly measure the presence of these
variants in a genome, we lack the framework to understand which of the variants impact
genomic function or how they interact with each other in living, breathing organisms. A core
mission of the IGVF Consortium is to identify variants that impact the expression of genes using
single-cell techniques and computational modeling. Applying a single-cell genomics approach to
selected diverse mouse strains can make a powerful contribution to the mission and to
resources of the Consortium. Our Center for Mouse Genomic Variation at Single Cell Resolution
will first use 38 mouse Collaborative Cross recombinant inbred lines that possess similar levels
of sequence diversity to humans to identify variants that influence gene expression levels and
chromatin accessibility at the single-nucleus level in 8 distinct tissues. We will sequence
simultaneously a subset of single-nuclei with both short-read sequencing and long-read
sequencing to identify variants that impact the expression of different transcript isoforms in
different cells across the different mouse strains. We will also measure the relationship of
variants in these CC Lines in the response of macrophages in these tissues in response to LPS
stimulation. The resulting resource catalogs of cell-type expression QTL, chromatin
accessibility QTL, splicing QTL, and response QTL maps will be useful for IGVF modeling
groups; for characterizing important variants; and for use by the wider community studying the
function of these tissues as well as for designing better pre-clinical models of human diseases.

## Key facts

- **NIH application ID:** 10474393
- **Project number:** 5UM1HG012077-02
- **Recipient organization:** UNIVERSITY OF CALIFORNIA-IRVINE
- **Principal Investigator:** Seyed Ali Mortazavi
- **Activity code:** UM1 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $2,534,261
- **Award type:** 5
- **Project period:** 2021-08-24 → 2026-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10474393

## Citation

> US National Institutes of Health, RePORTER application 10474393, Center for Mouse Genomic Variation at Single Cell Resolution (5UM1HG012077-02). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10474393. Licensed CC0.

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