Molecular Phenotyping and Genotyping Core

MOLECULAR PHENOTYPING AND GENOTYPING CORE: Abstract The objective of the Molecular Phenotyping and Genotyping Core is to support Joslin and external investigators in the study of molecular mechanisms of disease by providing equipment, expertise, and services in molecular phenotyping and genotyping, with a focus on technology-intensive and high-density data analyses, which would be too specialized or costly for individual laboratories to perform independently. One suite of services focuses on multi-analyte characterization of samples from human studies and includes services for DNA extraction, SNP genotyping, and genetic characterization of diabetes- and complications-related genes for clinical studies (next- generation sequencing-based assay). A second suite of services provides equipment and expertise for analysis of gene expression in cells and tissues including tissue homogenization, DNA shearing, Nanodrop spectrophotometer, Bioanalyzer analysis of DNA/RNA, custom library preparation and facilitated access to external sequencing facilities, and realtime and digital droplet PCR. The third suite of services assists investigators in metabolic phenotyping by providing a Seahorse bioanalyzer for metabolic rate determinations and a MALDI biotyper for identification and taxonomic classification of bacteria by high-throughput proteomic analysis. In each of these areas, the Core provides training and consultations to facilitate understanding and use of new methodologies by the Joslin community. Core staff work closely with Joslin’s institutional Bioinformatics and Biostatistics Core staff to facilitate rigorous analytical pipelines for -omics data analysis and secure data storage. The core is highly utilized, providing services to the majority of Joslin Research Base investigators, and productivity is evidenced by numerous high impact publications that cite core use. In the present application, in response to technological advances and the needs of our Research Base, we propose to enhance the Core’s capacity to support study of the molecular mechanisms of disease by providing the following new and ehanced services: 1) Single cell and single-nucleus RNA-sequencing; 2) expansion of the “genetic characterization for clinical studies” service, with addition of newly-identified genes for monogenic DM, and new SNPs for T1D, T2D, and complications; 3) automation of RNA extractions by acquisition of a Qiacube instrument; and 4) Integration of the Core’s curated DNA collection with the Clinical Translational Research Core’s Biorepository. These new initiatives, coupled with current services and training programs, will facilitate the access of Joslin investigators to state-of-the art phenotyping and genotyping that are instrumental for both basic, translational, and clinical research studies.