Genomics Shared Resource

GENOMICS SHARED RESOURCE - PROJECT SUMMARY/ABSTRACT The Genomics Shared Resource (GSR) integrates our legacy Genomics, Epigenomics, Computational Genomics and Molecular Cytogenetics core facilities. As a result of this integration, we have combined the activities and expertise of individuals in core facilities performing closely related work into a unified entity that enhances efficiency and quality of services so that cancer researchers can hand off samples to core personnel and receive analyzed data, providing a complete workflow housed in a single facility. The GSR is now implementing long-read sequencing services in addition to short-read services. When appropriate, we facilitate outsourcing of short-read sequencing to low-cost commercial providers. However, we have recently purchased the Illumina NextSeq 2000 platform that upgrades our short read sequencing capabilities. This investment anticipates a substantial drop in reagent costs in the next 1-2 years and migration of some of the currently outsourced sequencing back into the GSR. The GSR has also been proactive in optimizing new single cell assays for researchers with a current focus on single cell RNA-sequencing and chromatin assays as well as spatial transcriptomics of tissue sections. Cost savings through multiplexing for single cell experiments on the 10X Chromium platform has been used to make these assays substantially more cost-efficient, while reducing batch effects. Single cell sequencing combined with cell surface marker studies are being provided using the Mission Bio Tapestri platform, which is a foundation for ongoing clonal hematopoiesis research. We have increased our focus on collecting genomics data as a resource within the GSR. Our new institutional arrangement with Caris Life Sciences to perform exome and transcriptome sequencing on our Bronx cancer patients is accompanied by a research protocol to allow the primary sequence data to be returned to our FISMA-compliant data storage and computing resource. These data are made available under well-defined and well-established IRB protocols for researchers, to gain insights into the genomic events occurring in the Bronx patient population. Our goals for the next funding period will be to continue to support MECCC researchers in their genomic assays and data analyses. We are continuing to develop and support new assays, invest in new equipment, and help analyze data generated in the GSR. Investigators are encouraged to contact the leaders of the GSR and Biostatistics colleagues to discuss study design before initiating a project. For data analytical services, we will continue to train lab personnel to process data independently and can troubleshoot problems with researchers. Finally, a new goal is to tailor our services so that they provide novel insights into the cancer genomics of our Bronx population.