Data Management and Bioinformatics

PROJECT SUMMARY/ABSTRACT – DATA MANAGEMENT & BIOINFORMATICS CORE The Biomarkers of Atopy Beginning Early (“BABE”) U19 proposal seeks to compare how the immune system develops in the first year of life in populations at high risk vs. low risk for allergic disease with an emphasis on immunity at mucosal compartment, the site of exposure to allergens and the microbiome. Particularly, the

program compares urban Rochester infants; those who develop atopic diseases with Rochester infants protected from atopic diseases and Old Order Mennonites (OOM), a population practicing traditional, single-family farming with a low rate of AD and FA serve as an external comparison group for traditional, protective immune

development, in a birth cohort. The BABE consists of three individual projects and two cores, Cohort Admin and Biorepository core and Data Management and Bioinformatics (DMB) core. BABE will collect large-scale high- throughput data from our previously recruited cohort and a new cohort at multiple time-points within the first year

of life along with clinical endpoints. The high-throughput assays will be performed on cord blood, and infant stool, blood, infant skin swabs and tape strips and infant buccal swabs. The data collected includes metabolites, proteomics, transcriptomics, ATACseq, immune phenotyping, cytokine response, and microbiome (16S and

metagenomics). The DMB led by Dr. Juilee Thakar will support the data management, bioinformatics analysis and complex data analysis needs of Projects 1, 2 and 3, and Cohort Admin and Biorepository core. In addition, the core will collaborate with project investigators on experimental design and reporting, and provide a training

environment for project personnel on software tools and principles of methods and interpretation of results. By making data Findable, Accessible, Interoperable and Reusable (FAIR), the DMB will maximize the impact and optimize the path to identifying high impact insights. Specifically, DMB will: (1) Provide data collection, formatting

and storage infrastructure to facilitate data analysis and distribution across participating academic centers. (2) Support sharing of data by submission to the ImmPort repository and other relevant public repositories (e.g., SRA, dbGAP, Metabolomics Workbench). (3) Provide bioinformatic and statistical support in experimental design

and data analysis. (4) Provide support for data integration across projects between each data type. (5) Develop Integrated Score for Early Atopic Diseases (ISEAD). (6) Develop supervised and semi-supervised predictive models for atopic and food allergy outcome. (7) Develop mechanistic dynamic models of infant immune

development and skin health. Thus, DMB will play a critical support role in ensuring success of BABE.