# Genomic Resources for the Collaborative Cross

> **NIH NIH U24** · UNIV OF NORTH CAROLINA CHAPEL HILL · 2022 · $340,526

## Abstract

Genomic Resources for the Collaborative Cross
In response to NIH FOA PAR-17-273
 PI: Leonard McMillan
We propose to develop unique and unprecedented genomic resources for the experimental genetics
community in support of the Collaborative Cross (CC). The CC is an emergent genetics resource
consisting of more than seventy new isogenic mouse strains with genomes derived from eight founders
that captures most of diversity in Mus musculus. As reported in June’s issue of Genetics, we have
recently done full-genome sequencing for samples from each CC strain. The Aims of this proposal will
be:
1. To assemble and annotate unique individual genomes for each reproducible CC strain.
2. To provide tools that aid in experimental designs using the CC. In particular, how to design
 recombinant inbred intercrosses, that provide a sufficiently sized set of balanced and
 reproducible outbred samples. We will also provide tools that fix particular genes for testing
 against variable genetic backgrounds.
3. We propose to develop custom -omics analysis pipelines that leverage the unprecedented
 genomics annotation available for the CC to support the exploration allele specific effects.
Our primary goal is to bootstrap the use of the CC within the medical research community, with the
hopes that after the five years of support these resources will be self-sustaining through selling mice by
the UNC System’s Genetics Core facility.
This proposal has two Principal Investigators (PIs). The contact PI is Professor Leonard McMillan from
UNC’s department of Computer Science. He is joined by PI Fernando Pardo-Manuel de Villena, PhD. Dr.
McMillan has been the primary bioinformatics expert and tool developer for the CC over the past 8+
years of its development. Dr. Pardo-Manuel de Villena is a geneticist who led the development of the
Collaborative Cross. Together we bring extensive expertise in computational biology, genetics, and
genomics to ensure that the CC is the premier mammalian genetic reference population and a source of
new mouse models of human disease.

## Key facts

- **NIH application ID:** 10443545
- **Project number:** 5U24HG010100-05
- **Recipient organization:** UNIV OF NORTH CAROLINA CHAPEL HILL
- **Principal Investigator:** Leonard McMillan
- **Activity code:** U24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $340,526
- **Award type:** 5
- **Project period:** 2018-05-17 → 2023-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10443545

## Citation

> US National Institutes of Health, RePORTER application 10443545, Genomic Resources for the Collaborative Cross (5U24HG010100-05). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10443545. Licensed CC0.

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