# Bioinformatics Core

> **NIH NIH U54** · UNIVERSITY OF CALIFORNIA AT DAVIS · 2023 · $40,233

## Abstract

PROJECT SUMMARY
The overall objective of the proposed Diversity PDX Development and Testing Center (D-PDTC) is directed at
improving cancer precision medicine approaches for gastric and lung cancers. This will be achieved through the
large-scale development and molecular characterization of over 120 new minority gastric and lung PDX tumor
models and to utilize these for in vitro and pre-clinical PDX trials to test the efficacy of molecularly-matched
therapeutics administered as single agents or combination. Statistical testing for drug-responsiveness will be
performed, as well as the application of data integration strategies that relate treatment responses with molecular
characteristics of individual PDXs and patients’ tumors. The goal of Bioinformatics Core (UBC) is to provide
extensive data analytic support for the proposed studies at multiple stages including study design, molecular
characterization of the PDXs, target selection, and statistical correlation and modeling of drug responses. The
UBC will be established, and have considerable capabilities, by bringing together key personnel with strengths
in genomics, bioinformatics, and biostatistics, and by leveraging the existing infrastructure at the UCD
Comprehensive Cancer Center, specifically the Biorepository, Genomics, and Biostatistics Shared Resources.
The UBC will facilitate the seamless integration of our U54 through dynamic interactions with its investigators,
and via the implementation of a dedicated UCaTS Bioinformatics Core relational database that will serve as a
data repository and interface for linking project design, sample tracking, data analysis, and eventual data sharing.
For genetic characterization of the PDX models, and associated patient tumors, we will apply a suite of
established bioinformatics analysis pipelines implemented on a high-performance ultra-rapid next-generation
sequencing data analysis platform for processing whole-exome sequencing and RNA-sequencing data to
generate the fundamental results datasets consisting of fully annotated 1) genomic variants and 2) transcripts
with corresponding expression values. Additional tumor properties that can figure prominently in guiding
therapeutic decisions, such as mutational burden will also be defined. Subsequently, integrative bioinformatics
approaches will be applied for target prioritization and treatment matching, which will be followed by biostatistical
analyses to evaluate both drug responses and the accuracy of novel molecular biomarkers. The UBC will also
collaborate with the PDXNet, PDMR-FNLCR, and PDTCs for data sharing and participation in PDX trials.

## Key facts

- **NIH application ID:** 10733394
- **Project number:** 1U54CA283766-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA AT DAVIS
- **Principal Investigator:** CLIFFORD G TEPPER
- **Activity code:** U54 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $40,233
- **Award type:** 1
- **Project period:** 2023-08-01 → 2028-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10733394

## Citation

> US National Institutes of Health, RePORTER application 10733394, Bioinformatics Core (1U54CA283766-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10733394. Licensed CC0.

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