Core C: Immune bioinformatics and biostatistics

Nathanson, Katherine

Abstract

The Immune Bioinformatics and Biostatistics (Core C) will provide critical infrastructure and shared resources of biostatistic and bioinformatic expertise for the design, conduct and analyses of the Research Projects within the P01 - ?Radiation and Checkpoint Blockade for Cancer Immune Therapy.? Core C will provide services to P01 projects at every stage of research. Core members will: 1) consult with investigators on selection of study designs; 2) develop a relational database to store clinical trial patient correlative data for analysis; 3) generate DNA and RNA-based massively parallel sequencing data from tumors, exosomes, PMBCs (T cells), and tumor infiltrating lymphocytes; 4) conduct efficient and robust data analyses, utilizing both bioinformatics and biostatistics; 5) perform higher level secondary and integrative analyses using multiple pre-clinical and clinical data types; 6) create graphs and tables, assist investigators with the preparation of progress reports, presentations and manuscripts; 7) consult on the design of subsequent research; and 8) be responsible for the implementation of the Shared Resources Plan in regards to Genomic Data Sharing. These goals will be implemented through the following specific aims ? Aim 1) To provide biostatistical expertise in design and analysis for the proposed projects;
Aim 2) To provide support for the generation and initial analysis of DNA- and RNA-based massively parallel sequencing data;
and Aim 3) To perform secondary and integrative analyses across platforms and data types. A major theme of the P01 is studying the effect of checkpoint blockade and radiation therapy in humans through clinical trials, and concurrently performing linked pre-clinical studies in mice. Core C members will play a vital role in facilitating the comparison between the two groups, as they will be involved in the same analyses on human and mouse samples providing a conduit of knowledge between Projects. Core members have extensive experience in clinical trials biostatistics, database design and implementation, performance of massively parallel sequencing, bioinformatics analysis, and the utilization of analytical techniques for integration of the multiple data types generated from the Projects. The Immune Bioinformatics and Biostatistics Core will serve as an essential resource for the P01, providing specialized expertise to allow investigators to complete their research in a robust and efficient fashion. Members of Core C will work in a synergistic and cooperative fashion with Project investigators to determine the safety, efficacy and mechanism of the combination of local radiation therapy and immune checkpoint blockade and to understand the immunologic and genetic features of pre-clinical and clinical samples that are determinants of response, resistance, and relapse.

Public Health Relevance

The Immune Bioinformatics and Biostatistics (Core C) is an integral part of the P01. Core C supports all of the Projects and interacts with Core B, providing important links between pre-clinical and clinical studies in mice and humans, respectively. Core C will enhance the productivity of the P01 investigators by providing them with access to a biostatistics/bioinformatics team with expertise ranging from biostatistics support for clinical trials to generation and analysis of multiple types of massively parallel sequencing (e.g. whole exome and ATAC-Seq) to multi-platform data integration.