Genome Sequencing Facility (GSF)

Welcome

The Genome Sequencing Facility (GSF) at Greehey Children’s Cancer Research Institute (Greehey CCRI) at UT Health San Antonio (UTHSA) utilizes state-of-the-art genomic platforms to generate high-quality genomic data and provides support with its analysis.

About the Facility

The GSF provides Illumina next-generation sequencing (NovaSeq, NextSeq, and MiSeq platforms) and 10X Genomics single cell analysis for researchers inside and outside the Institute, University, and other academic institutions and companies. GSF offers two types of partnerships: research collaboration and fee-for-service. We vigorously promote active collaboration on concrete and sustainable research activities that mutually benefit GSF’s long-term success and our Next-Generation Sequencing (NGS) users.

The GSF was created in 2011 at the Greehey CCRI upon approval from the UT Health San Antonio Long School of Medicine, 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 turnaround time, GSF has established a track record with wide user bases from 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 have continuously and rapidly increased annually. Due to increasing requests and demands of NGS applications to cancer research, the GSF was recruited in 2014 as a new UT Health Cancer Center Shared Resource, as Next Generation Sequencing Shared Resources (NGSSR) at UT Health San Antonio, supported by Cancer Center Support Grant (CCSG P30: CA054174). The CCSG was successfully renewed in August 2020 for another five years, and the NGSSR was rated “Outstanding” by the study section.

In March 2016, Dr. Zhao Lai was awarded a $600,000 NIH Shared Instrument grant (S10 grant 1S10OD021805-01) to purchase Illumina HiSeq 3000 to upgrade the sequencing platform. Illumina HiSeq 3000 has provided our NGS users the greater efficiency in terms of high throughput, faster turn-around-time, and less expensive. Since the instrument upgrade in 2016, the number of active users of the GSF has continued to grow rapidly. In May 2016, Dr. Yidong Chen was awarded a $3.7M CPRIT Core facility award (RP160732) to upgrade and expand NGS capacity and further accelerate the adoption of high-throughput technology in translational cancer genetics and epigenetics research at UTHSCSA and the South Texas region. Illumina NextSeq 500 was acquired by funding support of CPRIT in February 2017. The NextSeq 500 provides a fast-sequencing turnaround time for an individual project. In June 2021, Dr. Lai was awarded her second NIH Shared Instrument grant with $600,000 (S10 grant 1S10OD030311-01) to upgrade to Illumina NoveSeq 6000 system to improve the GSF’s sequencing capacity significantly. In September 2022, Dr. Yidong Chen successfully renewed the CPRIT Core facility award (RP 220662). We are very grateful to NIH and CPRIT‘s funding support to continue the GSF’s NGS journey in the new exciting direction.

The GSF provides complete project consultation for optimal experimental design and setup. The GSF is also a research group with experience in customizing experiments and developing new protocols that leverage the latest advances in genomic technology.

We welcome opportunities to partner on many kinds of research projects regardless of size, both as scientific collaborations and on a fee-for-service basis. If you are considering next-generation sequencing for your research, please contact GSF director Dr. Lai for research collaboration or consultation on experimental design, pricing, and scheduling.

Contact us to discuss how we can help with your research.

Our Mission

The primary missions of the GSF are to:

• Provide Greehey Children’s Cancer Research Institute, Mays Cancer Center, and University of Texas Health Science Center faculty access to high throughput next-generation sequencing technology and bioinformatics support, with a high-quality service & research and highly competitive and comparable price.
• Support the development of genome-enabled research projects, scientific programs, and grant proposals.
• Education and training on NGS-focused genomics approach for the future generations of scientists.

Publication Acknowledgement

The facility should be listed in the “Acknowledgements” section of any publication using data generated in the Genome Sequencing Facility as follows:

Data was generated in the Genome Sequencing Facility, which is supported by UT Health San Antonio, NIH-NCI P30 CA054174 (Cancer Center at UT Health San Antonio) and NIH Shared Instrument grant S10OD030311 (S10 grant to NovaSeq 6000 System), and CPRIT Core Facility Award (RP220662).