Genomics and Genomic Analysis Core

PROJECT SUMMARY/ABSTRACT The purpose of the Genomics Core is to provide instrumentation, computational infrastructure, technical and analytic expertise, and guidance in order to broadly enable and to enhance the use of genomic analysis in Cystic Fibrosis (CF) research. Among other areas of research focus, the Genomics Core places a special emphasis in understanding of the microbiology and molecular physiology of people with CF (PWCF) in the post-CFTR modulator era. The Aims of the Core are to: 1) Provide advanced services to understand gene expression and molecular physiology of human cells that are relevant to CF disease states, 2) Provide cutting-edge sequencing and computational resources to study microbial communities in the CF gut, 3) Provide cutting- edge sequencing and computational resources that advance research on microbes and host-microbe interactions associated with CF disease states, and 4) Develop and support novel technologies to advance genomic research in CF. These aims will be fulfilled by providing UW CF researchers with consultative, production, and analytical services relevant to the following domains: 1. Transcriptome sequencing (conventional and single cell RNA-Seq) and targeted gene expression analysis (qRT-PCR). 2. Microbiome analysis through 16S rRNA profiling, taxon-specific qPCR, droplet digital PCR, and metagenomic sequencing. 3. DNA sequencing of microbes for whole genome analysis, genetic variant identification, and variant interpretation. 4. Genome-scale genetic screens using transposon mutant sequencing (Tn-Seq) and defined transposon mutant libraries. 5. New sequencing technology innovation. 6. Data analysis, management, and integration, including consultation on interpretation of genomic data and training in genomic methods. These capabilities will help illuminate the mechanisms and pathophysiology of extrapulmonary and respiratory CF diseases, informing novel strategies for the prevention, treatment, and diagnosis of those illnesses. We also aim and to understand how the administration of highly effective CFTR modulators changes the physiology of host cells, and the composition and metabolic functions of the microbiome and its interactions with host individuals.