# Biospecimen and Data Core

> **NIH NIH U54** · STANFORD UNIVERSITY · 2023 · $325,920

## Abstract

ABSTRACT/SUMMARY: BIOSPECIMEN AND DATA CORE
Our CCSB will dissect how interactions between malignant, stromal and immune cells in the primary tumor and
lymph nodes (LN) influence systemic immunity and facilitate distant metastasis, across multiple cancer types.
Accordingly, the goal of our Biospecimen and Data Core is to provide expertise and facilities for fresh and
archived specimen acquisition, genomic and image data processing, and sharing. This will ensure the provision
of high-quality, richly annotated datasets that serve the needs of our Research Projects in mouse and human;
to make them widely available to the CSBC and broader community; and to integrate them with external data
sources. We will perform the following aims to fulfill our Center goals: (1) We will develop a fresh tissue
biospecimen repository of human head and neck cancer (HNSCC) and lung cancer, as well as mouse models
of metastasis for single cell RNA sequencing (scRNA-seq) and CODEX analysis. Human specimens including
matched primary tumor, LN and distant metastases (when available) from multiple tumor regions will be assigned
unique identifiers connecting them to human clinical annotations to develop and populate a HIPAA-compliant
REDcap database, while mouse specimens will be linked to detailed experimental information for cross-species
phenotypic validation and mechanism study. (2) We will construct TMAs of fixed primary, LN and distant
metastases with detailed clinical annotations in order to validate findings from our Research Projects on large
independent cohorts. Our TMAs will be constructed from treatment-naïve archived FFPE specimens for head
and neck cancer and lung cancer. The TMAs will consist of cores from primary tumors and uninvolved LNs from
LN-negative (N0) patients; primary tumors, involved and uninvolved LNs from LN-positive (N+) patients; and
distant metastases for a subset of LN-positive patients. Individuals’ tissues will be sampled at multiple locations.
The clinical follow-up (survival, occurrence of metastasis) will enable us to infer prognostic significance of our
work. (3) we will perform QC, processing, and basic analyses using existing robust pre-processing and analysis
pipelines for scRNA-seq, CODEX and IHC data. (4) we will leverage Center-generated data in the context of
larger publicly available cohorts. We will identify, curate, pre-process, and analyze public data relevant to the
Center’s aims, performing baseline meta-analysis of the relationship between gene expression data and
LN/distant metastasis which we can link to insights from our internally generated datasets. We will coordinate
with the broader CSBC to make data and analyses available, contribute to standardizing reporting of assay data,
and make computational tools widely available. Taken together, the centralization of the acquisition of single-cell
proteomic expression (CODEX), scRNA-seq, and spatial transcriptomic data for the two research projects in this
proposed BDC wil...

## Key facts

- **NIH application ID:** 10729469
- **Project number:** 1U54CA274511-01A1
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** JOSEPH B SHRAGER
- **Activity code:** U54 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $325,920
- **Award type:** 1
- **Project period:** 2023-09-19 → 2028-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10729469

## Citation

> US National Institutes of Health, RePORTER application 10729469, Biospecimen and Data Core (1U54CA274511-01A1). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10729469. Licensed CC0.

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