Assessing Individual Head and Neck Squamous Cell Carcinoma Patient Response to Therapy Through Integration of Functional and Genomic Data
Even though head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide, there are only two PD1 targeted immunotherapies (pembrolizumab and nivolumab) and one tumor intrinsic EGFR targeted therapy (cetuximab) that are FDA approved for treatment of HNSCC. Taking advantage of a high throughput inhibitor assay and computational tools originally showing success in leukemia, we designed and employed HNSCC-specific inhibitor panels that capture the diversity of aberrational pathways in HNSCC to test viable cells from patients’ HNSCC tumors. This provides a functional context to the multi-omic readouts conducted on these samples (mutations, protein expression and copy number alterations). In addition to generating this deeply characterized functional genomics datasets, we also developed additional analyses that have the potential to provide greater insight into patterns of drug response in HNSCC and potentially aid in evaluation and assessment of effective targeted therapeutic agents to support precision oncology tumor boards.
Citation: Bottomly, D., Mathieson, C., Vigoda, M., Jeng, S., Evans, N., Anderson, A., Blucher, A., Lesch, A., Zheng, C., Laderas, T., Jacobs, J., Kulesz-Martin, M., McWeeney, S. (In Preparation) Assessing Individual Head and Neck Squamous Cell Carcinoma Patient Response to Therapy Through Integration of Functional and Genomic Data.
Workflow
Code to reproduce manuscript figures/tables is available here
Processed Data
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- Clinical
- Clinical Dictionary
- Gene-level CNA
- RNASeq counts
- WES/targeted Sequencing Mutation Calls
- Inhibitor AUC values
- Drug target information
Results
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- Response Cards for all patients
- Alteration Network Prioritization plots for all patients
- Table of Network prioritization results
Frequently Asked Questions
- Q: How do I access the raw sequencing and array data?
- A: FASTQ and Cytoscan HD CEL file access can be requested from from dbGaP: phs003456.v1.p1
- Q: Licensing
- A: The processed data provided here is licensed under: CC-BY-4.0