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 in pediatric cancer genomics 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, by providing superior sequencing performance and fast project turnaround time, GSF has established a track record with a wide user base, including 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 increased rapidly each year. Due to increasing requests and demands for NGS applications in cancer research, the GSF was recruited as a new Cancer Center Shared Resource, the Next Generation Sequencing Shared Resource (NGSSR), at UT Health San Antonio in 2014, supported by the Cancer Center Support Grant (CCSG, P30: CA054174). Since then, the NGSSR has been an integral part of the Shared Resources of MCC and CCSG, strongly supporting 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, including an Eppendorf EPMotion 5750 automation system, through 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, the GSF, with CPRIT grant support, 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 with spatially resolved whole-transcriptome gene expression profiling to localize and quantify gene expression in the tissue context. In 2025, GSF Director Dr. Lai was awarded an NIH S10 grant (S10OD038331) to acquire a 10x Genomics Xenium Analyzer, enabling researchers to conduct spatial transcriptomics and proteomics on tissue specimens at cellular and subcellular resolutions. We are very grateful to NIH and CPRIT for their funding support in continuing GSF’s NGS journey into a new, exciting direction.