Sequencing and Informatics

PROJECT SUMMARY: SEQUENCING & INFORMATICS MODULE The Vanderbilt Vision Research Center (VVRC) includes faculty investigators with a strong interest in discerning genetic relationships that govern functional circuits in the visual pathways and those that predispose patients towards disease and response to treatment. These relationships require the ability to measure expression and genomic patterns in large numbers of samples, transgenic animals, and even within individual cells. The purpose of the VVRC Sequencing & Informatics Module is to provide a comprehensive resource for all genetic, genomic, and bioinformatic research that utilizes animal or human RNA or DNA. This module gives investigators and their staff access to state-of-the-art genomics and bioinformatics facilities, software and technical expertise through subsidized scholarship use of the Vanderbilt Technologies for Advanced Genomics (VANTAGE) and Vanderbilt Technologies for Advanced Genomics Analysis and Research Design (VANGARD) core resources. VANTAGE performs a wide array of high-throughput DNA and RNA services, while VANGARD is housed within the Center for Quantitative Sciences and provides biostatistical and bioinformatic support of experimental design and data analysis and storage. VVRC support translates on a dollar-for-dollar basis to scholarships issued to VVRC investigators applicable for all VANTAGE/VANGARD services. This scholarship system is implemented by the VUMC Office of Research and is utilized instead of a discount or co-pay via the VUMC ILab accounting system. In the current funding cycle, the Sequencing & Informatics service was used for 69 publications involving 19 investigators, including 7 current NEI R01 holders. Projected use of the service module is considerable, with 9 of 16 current NEI R01 grant holders projecting moderate (6) to extensive (3) use of the core. All told, 22/52 VVRC members will have moderate to extensive use (42%). The Sequencing & Informatics Module, housed in a centralized location conveniently accessed from all parts of campus, is directed by VVRC Director David Calkins, PhD. Using resources and personnel supported in part by this Core mechanism, the VVRC Genomics Module will provide (1) next- generation sequencing paradigms suitable for visual system tissues, (2) state-of-the-art genotypying services, (3) DNA extraction, DNA sample banking and other services that support high-throughput preclinical and clinical genetics studies, and (4) bioinformatics support for genomics data. These services and resources will enhance the scope of experimentation NEI-funded VVRC investigators conduct, expand the training of students and fellows involved in vision science, and promote collaboration by providing sophisticated, high- resolution and high-throughput genomics and bioinformatic services to those who otherwise would not have such capabilities, including early-career vision scientists and clinician-scientists competing for extramural funding for their laboratories.