# Core 2: Immune Bioinformatics and Computational Biology Core

> **NIH NIH P01** · MASSACHUSETTS GENERAL HOSPITAL · 2020 · $181,107

## Abstract

PROJECT SUMMARY (IMMUNE BIOINFORMATICS AND COMPUTATIONAL BIOLOGY CORE)
The overall goal of this P01 proposal is to apply a systematic approach to understanding mechanisms of
immune resistance that can guide the rational design of novel combinatorial immunotherapies to effectively
treat head and neck squamous cell carcinoma (HNSCC) patients. To accomplish this goal, we will use several
cutting-edge bioinformatics strategies on data from bulk and single cell RNA sequencing (scRNA-seq),
epigenomics assays, and exome sequencing, as well as biostatistics analysis of clinical trial data. Our team
has complementary expertise encompassing HNSCC genetics and biology, innate and adaptive immune
response, immune bioinformatics, single cell dynamics and the analysis of scRNA-seq, cancer epigenomics
and genome-wide regulatory data, and HNSCC clinical trial data analyses. The objective of the Immune
BioInformatics and Computational Biology (IBCB) Core is to provide, disease-specific comprehensive
and innovative support to the P01 investigators for the study design, analysis, integration and
interpretation of a broad range of omics-based and clinical trial studies.
The IBCB Core will support the three projects of the P01 through four specific aims. First, we will recommend
strategies for study design and provide analyses specific to immune bioinformatics. This includes, but is not
limited to, mutational burden analysis and neoantigen prediction, analysis of HLA class I alleles, and immune
cell type deconvolution. The second aim is to provide expertise for study design and perform various analyses
and methods development for single cell bioinformatics. We will utilize several recently developed scRNA-seq
methods for QC, batch correction and normalization, imputation, innovative visualizations, automatic cell type
identification, and differential expression testing. The third aim is to provide consultation on experimental
design and provide analyses for epigenomics data. We will analyze genome-wide DNA methylation and
transcriptomics data before and after different immune checkpoint blockade (ICB) therapeutic regimens. Aim
four is to provide advanced biostatistics and bioinformatics support for clinical trial analyses, power analyses,
and other bioinformatics support not mentioned above, including data management, transparency, and data
sharing.

## Key facts

- **NIH application ID:** 10020930
- **Project number:** 5P01CA240239-02
- **Recipient organization:** MASSACHUSETTS GENERAL HOSPITAL
- **Principal Investigator:** Ramnik J Xavier
- **Activity code:** P01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $181,107
- **Award type:** 5
- **Project period:** 2019-09-19 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10020930

## Citation

> US National Institutes of Health, RePORTER application 10020930, Core 2: Immune Bioinformatics and Computational Biology Core (5P01CA240239-02). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10020930. Licensed CC0.

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