Sequencing and Genotyping Facilty

Since August 2011, the SGF has been led successfully by Dr. Riccardo Pappa, Assistant Professor of Biology at the UPR Rio Piedras Campus. Dr. Pappa is proficient in the operation of the SGF instruments and NGS data analysis, since he uses these technologies in his own research project. The SGF was officially created in 2006 through a combination of funds from different grants, including NCRR AABRE Grant #P20 RR16470, NIH-SCORE Grant #S06GM08102, NSF-CREST Grant #0206200, and NINDS-SNRP U54 NS39405 and institutional matching funds. The main goal of the SGF is to provide researchers, students and faculty from Puerto Rico and the Caribbean access to state-of-the-art equipment, technology and technicians who are committed to helping investigators produce the highest quality data. Presently, the SGF is the largest and most active genomics facility in Puerto Rico. The Sequencing and Genotyping Facility (SGF), is designed to: 1) provide students and researchers in Puerto Rico with access to advanced equipment for collecting high-quality automated sequence and genotype data; 2) training and advising researchers and students island-wide on how to obtain, archive, and analyze data; and 3) create an alliance of researchers and students who share core research technology and who work together to strengthen scientific infrastructure and research competitiveness within Puerto Rico.

Proposed Activities. Building on the growth experienced by the SGF in recent years, and the addition of Next Generation Sequencing (NGS) capabilities and outreach to network users, we are developing an undergraduate course schedule that will fully prepare laboratory workforce to effectively and efficiently use these cutting-edge technologies. In the proposed renewal period, the SGF will introduce hands-on training and technical aspects of NGS technology to the existing UPR Rio Piedras, Department of Biology Laboratory of Genetics (Biol 3350) course, currently offered to undergraduate biology students at the UPR Rio Piedras Campus. The SGF will continue to provide support in the preparation and submission of grant applications to the NIH, National Science Foundation (NSF), the National Aeronautics and Space Administration (NASA), the US Department of Agriculture (USDA), and other agencies to INBRE network users and will continue to provide support for the preparation of scientific, peer-reviewed manuscripts.

 

Table 1. Proposed Training Program for Sequencing and Genotyping Facility (SGF) Users

Type of UserTraining to be OfferedServices to be ProvidedOther Requirements
Undergraduate (UG), Graduate (G) students, technicians, postdoctoral trainees and faculty from the UPR System or INBRE-affiliated institutionsSample preparation required for Illumina Next-Generation Sequencing (NGS), analysis of sequencing results. Includes, DNA isolation, quantitation, QC, gel electrophoresis, Bioanalyzer and other accessory equipment use. For G students, technicians, postdocs and faculty, same as above but with all hands-on accessory applications leading to QC and bioinformatics aspect of NGS.For UGs, five-person training in NGS techniques. Accessory equipment use is limited to trainer. For G students, technicians, postdocs and faculty, same as above but trainees will go through hands-on QC preparation and analysis.Users are required to go through SGF terms and necessary safety procedures before proceeding.