PGC Visayas sees greater genetics capacity with new lab

PGC Visayas Bioinformatics Facility staff headed by Mr. Marlon John Varon (Science Research Specialist), Science Research Associates Ms. Julia Theresa Regalado, and Ms. Vanessa Joy Diamante shared their knowledge and expertise on bioinformatics with researchers from the Mindoro State University in September 2022. (Photo from PGC Visayas FB page)

By Joseph B.A. Marzan

The Philippine Genome Center-Visayas (PGC Visayas) at the University of the Philippines Visayas (UPV) in Miagao, Iloilo expects to increase its capacity in genetics research as it launched a new laboratory on Tuesday, Nov 29, 2022.

The new Bioinformatics Laboratory of the PGC Visayas boasts high-powered servers and state-of-the-art computing technology that aids the center in determining the genetic makeup of an organism or a virus down to the species level.

This includes bioinformatics servers and computer workstations, which they started to procure in 2019.

PGC Visayas also capacitated its personnel through bioinformatics with PGC’s primary hub at UP Diliman in Quezon City also in 2019.

Bioinformatics analysis and training services of the PGC Visayas through the new lab include:

–          Deoxyribonucleic acid (DNA) barcoding, a tool for rapid species identification based on DNA sequences, efficiently recognizing known species and speeding up discovery of new ones;

–          Metagenomic analysis which allows to provide analysis of the composition and abundance of species and genome components, generate a non-redundant catalog of genes, take note of functions of genes, and comparative analysis of samples;

–          Transcriptomic data analysis may allow the identification of candidate genes and those associated with traits of interest in gene analysis;

–          Whole genome data analysis where genomes can be examined using the de novo sequence if there is no available reference sequence or no known genomes of significant variations are expected;

–          Custom workflow; and

–          Programming and basic scripting.

With this new laboratory, the center is looking to become a regional and national leader in omics research in the fields of fisheries, marine sciences, and allied disciplines.

The new lab is part of the Establishment of Genomics Consortium and Core Facility in Visayas Project, with funding support from the Department of Science and Technology- Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development (DOST-PCAARRD) which allowed them to increase and enhance their human resources.

PGC Visayas Director Victor Marco Emmanuel Ferriols said that even before the launch, the laboratory has been helping the region in fighting the coronavirus disease 2019 (COVID-19).

Ferriols pointed out that the center helped detect variants of the Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2), the virus which causes COVID.

Some of the variants detected by the PGC Visayas include the Omicron and Delta variants, which worried the populace earlier this year because of their stark variation from the original virus and resistance to vaccines.

“Our bioinformatics team, working in tandem with the PGC Biosurveillance Team, has been working tirelessly since January [2022], sacrificing even their weekends in order to provide up-to-date information about COVID-19 variants to the [Department of Health] in order to guide both regional and national policies,” Ferriols said.

“With the establishment of the [PGC Visayas] and with [the] latest addition of the bioinformatics laboratory, I am confident that we will be facing the future prepared, whatever challenges we may face,” he added.

UPV Chancellor Clement Camposano said in his message that the launch was indicative of UPV’s upgrade as an institution of higher learning.

The chancellor connected this to another recent development, the institutionalization of the UPV Regional Research Center, saying that this further upgrades the university’s and the PGC’s own existing research capabilities.

He added that this new laboratory will enable the university to become a leader in collaborating for greater capabilities of other higher educational institutions, something which he observed was still lacking in UP.

“There is one other aspect of leadership which the university has yet to fully explore, and that is leadership that involves the building of capacities in other institutions. That is one area where the university needs to do more work,” he said.

“As a facility, from its very conceptualization, [the PGC Visayas Bioinformatics Laboratory] is actually based on collaboration. […] I believe that it is through collaboration that [UP], and [UPV] in particular, can exercise leadership. Through this laboratory, we will be able to support the growth and development of our partner institutions of higher learning,” he added.

Camposano said that the PGC Visayas’ long-term goal is to set up a network of research institutions among partner state universities and colleges and other higher education and research institutions to provide a greater focus on the use of genomics in various research fields through appropriate trainings and workshops.