# Core C

> **NIH NIH P30** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2024 · $571,396

## Abstract

Project Summary (Core C: Genotyping, Analysis and eQTL Core)
 The purpose of this core is to provide genotyping and analysis services for the supported grants.
Analysis services will focus on genome wide association studies (GWAS) that are intended to identify the
relationships between genotypes and phenotypes with the ultimate goal of implicating specific genes that
influence substance use disorder (SUD) relevant traits. The wet-lab protocols and bioinformatic pipelines used
by this core have already been established, but they will continue to be improved over the course of the
funding period. We will also continue to provide expression quantitative trait locus (eQTL) mapping, presenting
these results on a public facing website and also incorporating them into the GWAS results. This core will also
perform the wet-lab and bioinformatic steps necessary for phenotype prediction in support of RATTACA (RAT
Trait Ascertainment using Common Alleles), which is described in Core B.
 One of the key services that this core will offer is the ability to genotype heterogeneous stock (HS) rats
at millions of polymorphic markers with an accuracy of >99.75% at an extremely low cost. We will accomplish
this by performing low coverage whole genome sequencing (lcWGS) followed by an imputation step that uses
the deep sequence data that are available from the 8 inbred founders of the HS population. This approach has
undergone multiple improvements over the past decade. We have used this approach to genotype HS rats,
Sprague Dawley rats, various outbred mouse populations and most recently zebrafish; however, the purpose
of this core is to genotype HS rats for supported grants. We will continue to improve this pipeline by inputting
tandem repeats and structural variants and by calling genotypes on the Y and mitochondrial chromosomes.
 In addition to genotyping HS rats, this core will perform genetic analyses, which include GWAS,
phenome-wide association studies (PheWAS), heritability estimates, genetic correlations and related
approaches. We have already demonstrated our ability to perform these analyses and will offer them as a
service to supported grants. Results are summarized in “reports'' that provide figures and tables that can be
incorporated directly into publications. These reports are one of the primary outputs of this core and would be
extremely difficult for the supported grants to develop independently because they require substantial
statistical and computational expertise.
 Finally, this core will support two public facing websites. The first provides the only available eQTL
resource for rats. The second will introduce, for the first time, a public facing transcriptome wide association
studies (TWAS) portal, allowing investigators to query individual genes and discover correlations between the
genetically determined expression of that gene and all of the phenotypes in our HS rat database; the database,
which is supported by Core A, currently contains phe...

## Key facts

- **NIH application ID:** 10935613
- **Project number:** 1P30DA060810-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Abraham A. Palmer
- **Activity code:** P30 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $571,396
- **Award type:** 1
- **Project period:** 2024-09-01 → 2029-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10935613

## Citation

> US National Institutes of Health, RePORTER application 10935613, Core C (1P30DA060810-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10935613. Licensed CC0.

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