Sequencing and Genomics

ABSTRACT: SEQUENCING AND GENOMICS SHARED RESOURCE Sequencing and Genomics (SEQ) provides an integrated platform of technology, expertise, education, and infrastructure to create an accessible environment for LCCC researchers to undertake cutting-edge genomics projects. The Core specializes in six major technologies: Next Generation short-read sequencing (Illumina), long-read sequencing and genomic mapping (Oxford Nanopore Technologies, BioNano Inc.), NanoString digital RNA quantification, Affymetrix microarrays, Illumina bead array genotyping, and RNAi screening for functional validation. Through reciprocity with North Carolina State University, the SR also has access to the Pacific Biosciences Sequel system. These are complemented by LCCC investments in computational infrastructure and analysis. Over the past five years, LCCC has integrated two new units in partnership with TPF and CPDM to compliment SEQ, specifically to facilitate translational cancer genomics to seamlessly support the coordination, project management, and tracking necessary to perform genomics studies on patient samples from protocol-driven trials. In addition the Translational Genomics Laboratory (TGL) focuses solely on cancer sample preparation for downstream sequencing, NanoString analysis, or other molecular testing. This laboratory uses automated instrumentation and stable protocols optimized for limited input and degraded cancer specimens collected from clinical trials and translational studies. TGL initiates a pathway for clinical genomics projects through SEQ and subsequent analysis by the bioinformatics SR (BIOIN). SEQ SR requests $195,591, 3% of the total fiscal year 2019 budget. LCCC faculty were 43% of fiscal year 2020 users. During the past five years SEQ supported the LCCC investigators involved in TCGA. This project oversaw the molecular characterization of over 20,000 primary tumor and matched normal samples across 33 cancer types. Within the next year, SEQ will acquire an ONT PromethION 24 system, which uses a high- capacity, long-read sequencing technology capable of high production whole genome sequencing and transcriptomics. This technology allows for efficient resequencing of whole genomes including repetitive elements, structural variation, and other problematic regions of the genome. ONT sequencing provides reproducible detection of small, medium, and large size structural variations, and in the near future the detection of 5mC.