By establishing a Next Generation Sequencing (NGS) Center in late 2007, and being the first Illumina sequencing Certified Service Provider (CS-Pro®) in North America in 2008, NCGR and the NM INBRE Sequencing and Bioinformatics Core (SBC) are transforming the research of the INBRE network by providing de novo sequencing, resequencing and functional genomics applications of enormous translational impact. These include the molecular understanding of single-gene and complex disorders, cancer biology, traits of agronomic importance, environmental genomics and personalized medicine. This insight is achieved by combining NGS with the center’s sophisticated bioinformatics tools, software development, robust IT infrastructure and creative techniques for data mining and knowledge discovery.
The objective of the core is to provide the INBRE network with turn-key access to discovery-enabling sequencing and bioinformatics solutions, educational symposia, mentorship/internship programs and collaborative research support.
NCGR employs the latest methods and is a recognized Illumina and Agilent CS-Pro certified lab with sequencing instrumentation comprised of two HiSeq2000’s, a GAIIx, and a Pacific Biosciences RS partially funded by NM INBRE. The lab uses the PerkinElmer (Caliper) LCGX high-throughput nucleic acid assessment instrument in conjunction with the Sciclone NGS liquid handling robot to QC samples and prepare libraries in a high-throughput manner. Sequencing services include whole genome and transcriptome shotgun, ChIP, small RNA, mate-pair, ultra-low sample input (1ng) DNA, and targeted exome. Bioinformatics includes de novo assembly (transcriptome and genome), read count-based expression, variant detection, differential expression analysis and custom bioinformatics for challenging analysis problems. A competitive pilot study RFP mechanism is used to establish collaborations in the INBRE network to solve pressing research questions in various organisms and clinical areas.
Since 2008, over 45 INBRE collaborations have been created enabling 15 grant awards and 12 peer reviewed publications in the areas of basic science and environmental research, assessment and modeling of human disease (in traditional and emerging model organisms), de novo genome assembly and comparative genomics of agents of infectious disease, and biological studies in human disease.
The NM-INBRE SBC increases the research capacity of INBRE investigators and their competitiveness in attaining research grants and manuscript publications by providing cutting-edge discovery techniques, fruitful collaborations, a yearly educational New Mexico BioInformatics, Science, and Technology (NMBIST) symposium, and bioinformatics-based educational initiatives for elementary through graduate school students.