Data Analysis & Submission Core

University Of Pennsylvania, Philadelphia PA

Investigators

Abstract

ABSTRACT: Data Analysis and Submission Core The Data Analysis and Submission Core (DASC) will assemble and validate virome characterization data for the proposed Penn VCC and submit data to public repositories and the HVP Consortium Organization and Data Collaboration Center (CODCC). The Core will be led by Drs. Kyle Bittinger and Hongzhe Li, who have a well- established track record of collaboration spanning twelve years of published work, as well as extensive collaborations with other members of the Penn VCC. Data processing will be carried out within the Analytical Laboratory of the CHOP Microbiome Center, directed by Dr. Bittinger. The Analytical Laboratory has provided bioinformatics support to hundreds of projects since its establishment in 2015. Statistical analysis and multi- omics data integration will be led by Dr. Li, who has contributed extensive innovative new methods in this space. They will process sequence data in a timely fashion from diverse samples including nucleic acid sequencing from isolated virome preparations, metagenome and 16S sample types. They will assemble and annotate sequences, and carry out first pass statistical analysis. They will apply statistical and bioinformatic approaches to interrogate longitudinal stability or evolution of the virome over multiple-year periods in children and adults; to assess the relationship between oral, respiratory tract, gut and blood compartments; and apply and refine analytical techniques to distinguish authentic from environmental background in low microbial content specimens. The team will also carry out analysis of long read single molecule sequencing to improve contig assembly and assess phage covalent DNA modification; analyze HiC data to assign viruses to hosts; and process imaging data to yield viral counts and other forms of information. The team will assess the quality of virome purifications using ViromeQC. The team will work with the other VCCs and the CODCC to establish and validate common protocols for bioinformatics and data analysis, and transfer data to the CODCC in a timely fashion. To accomplish these goals, the Aims of the Penn VCC DASC are as follows: Aim 1. Carry out bioinformatics data processing and statistical analysis to characterize the human virome and validate results. Aim 2. Construct a virome database to integrate data from a multifaceted set of experimental and computational approaches. Aim 3. Coordinate with the CODCC to develop common data formats, harmonize tools and workflows, and submit data to public repositories.