The Genome Sequencing Facility (GSF) was created in 2011 by Greehey Children’s Cancer Research Institute (Greehey CCRI) in UT Health San Antonio upon the approval from the Medical School Dean’s office, with the acquisition of an Illumina HiSeq 2000 system. The GSF was originally a service facility supported entirely by the Greehey CCRI, with a focused mission for the genomics of pediatric cancer research. Since then, it has rapidly become a heavily utilized and well-functioning unit, used by many members of Greehey CCRI, the UT Health Mays Cancer Center (an NCI-designated Cancer Center, the only one in South Texas), UT Health San Antonio, and some other researchers in surrounding San Antonio institutions, including the University of Texas at San Antonio, Texas Biomedical Research Institute, Brooke Army Medical Center and U.S. Army Institute of Surgical Research. In addition, enabled by providing superior sequencing performance and fast project turn-around time, GSF has established a track record with wide user bases from many outside researchers.
Since its inception, the GSF has been one of the most utilized and efficient core facilities at UTHSA. The number of users and submitted samples has continuously and rapidly increased annually. Due to increasing requests and demands of NGS applications to cancer research, the GSF was recruited as a new Cancer Center Shared Resource, as Next Generation Sequencing Shared Resources (NGSSR) in UT Health San Antonio 2014, supported by Cancer Center Support Grant (CCSG P30: CA054174). Since then, the NGSSR has been an important integral part of the Shared Resources of MCC and CCSG to strongly support cancer-related genomic studies.
Over the years, the GSF has made substantial improvements to its genomic infrastructure. The GSF upgraded to an Illumina HiSeq 3000 sequencer via an NIH S10 grant (1S10OD021805) in 2016. In 2017, the GSF received funding for a NextSeq 500 sequencer and other equipment, such as Eppendorf EPMotion 5750 automation system, via a Cancer Prevention and Research in Texas (CPRIT) Core Facility Support Award (RP160732). The GSF replaced the Illumina HiSeq 3000 sequencer and upgraded to an Illumina NovaSeq 6000 via its second NIH S10 grant (1S10OD030311) and successfully renewed the CPRIT Core Facility Support Award (RP220662) in 2022. In 2023, the GSF purchased NextSeq 2000 to replace the previous Nextseq 500. To accommodate the increasing demand for single-cell analyses, in 2023, with CPRIT grant support, the GSF upgraded to a 10x Genomics Chromium X System to improve capacity and efficiency for single-cell sequencing. The 10x Genomics Chromium X System can process RNA FLEX samples, allowing single cell, nuclei, or tissue samples to be fixed and stored before library preparation, significantly enhancing our ability to manage these clinically related specimens. Meanwhile, with the same grant support, the GSF acquired CytAssist to enable first-time spatial transcriptomics analysis for users. CytAssist Visium technology, the first generation of sequencing-based ST platforms, combines histology and spatially resolved whole transcriptome gene expression profiling to localize and quantify gene expression in the tissue context. We are very grateful to NIH and CPRIT funding support to continue the GSF’s NGS journey to the new exciting direction.