Integrated Genomics

Case Western Reserve University, Cleveland OH

Investigators

Linked publications & trials

Abstract

INTEGRATED GENOMICS SHARED RESOURCE PROJECT SUMMARY/ABSTRACT The Integrated Genomics Shared Resource (Genomics SR) provides Cancer Center investigators with high throughput genomics technologies and cutting-edge bioinformatics services. This multi-site SR is jointly supported and managed by the Case Comprehensive Cancer Center, Case Western Reserve University (CWRU) School of Medicine, and Cleveland Clinic Lerner Research Institute (LRI). The SR provides access to a full spectrum of genomics technologies including Next Generation Sequencing (NGS) for DNA and RNA, as well as single cell genomics and spatial transcriptomics analyses. Multiple technology choices distributed at multiple sites, robust experimental design, and rapid access to a focused, well-executed data analysis pipeline ensures success of cancer genomics studies. To this end, the resources that comprise the Genomics SR work closely together and ensure that sequencing throughput bottlenecks are distributed among locations to provide prompt results for Case CCC investigators. During the current funding cycle, the Genomics SR provided services to 444 registered users, 41% of whom are Case CCC members that accounted for 59% of total usage, representing 5 Case CCC programs. The Genomics SR also offers guidance to cancer researchers in all phases of genomic research projects including experimental design, sample prep & quality control, data generation (NGS, genotyping, gene expression profiling, etc), and data analysis/interpretation. An example of a cohesive workflow in the SR includes single cell sequencing (10X Chromium Controller) or spatial analysis (10X Visium, NanoString GeoMx) in the Functional Genomic Core, followed by sequencing at either one of our genomic SR locations at CWRU or LRI (Illumina NovaSeq X-Plus or NovaSeq 6000 instruments). Data acquisition is followed by analysis provided by the bioinformatics component. The scientific impact of the Genomics SR is demonstrated by three publications that highlight specific services. RNAseq experiments determined the genes that are differentially regulated by JAB1 in osteosarcoma, single cell experiments showed mTOR signaling pathway disruption in TIM-3+ T cells and methylation array experiments demonstrated premature aging in HIV patients. Finally, the NovaSeq X-Plus combined with an Eppendorf robotic platform are also used to develop Clinical Whole Genome sequencing pipelines followed by tertiary variant interpretation pipelines and reporting. Through its comprehensive service offerings, the Integrated Genomics SR provides Case CCC investigators with outstanding genomics support greatly enhancing basic, translational and clinical research.