Biospecimen and Data Core
Joseph Shrager, MD, co-Lead
John Sunwoo, MD, PhD, co-Lead
Parag Mallik, PhD, co-Lead
Both Project 1 and Project 2 will use a shared resource core dedicated to the acquisition of patient samples and associated clinical annotation and data management. These efforts will yield highly multiplexed, multi-scale datasets that will be analyzed by novel bio-computational methods to reconstruct intracellular and intercellular molecular interaction networks to identify, then functionally validate, critical mediators of metastasis.
This Core will provide to all our Center researchers the expertise and facilities for fresh and archived specimen acquisition, genomic and image data processing, and data sharing.
- Develop a fresh tissue biospecimen repository of HNSCC and LUAD samples, as well as mouse models of metastasis for single-cell RNA sequencing scRNA-seq)and CODEX analysis
- Construct clinically annotated tissue microarrays of fixed primary, LN, and distant metastases to validate findings from Center projects on large independent cohorts
- Perform quality control, processing, and basic analyses using existing robust pre-processing and analysis pipelines for scRNA-seq, CODEX, and immunohistochemistry data
- Leverage Center-generated data in the context of larger publicly available cohorts as well as identify, curate, pre-process, and analyze public data relevant to the Center’s aims. Baseline meta-analyses of the relationship between gene expression data and LN/distant metastasis will be linked to insights from internally generated datasets.
All data and analyses will be available to the broader CCSB consortium.