By Eden Estopace,  03/03/2015,

With the opening of the Philippine Genome Center (PGC) in 2012, basic and applied research for health diagnostics, therapeutics, DNA forensics and drug discovery has started to gain momentum in the country.

Today, the center has two core facilities – the DNA Sequencing Core Facility (DSCF) and the Bioinformatics Core Facility (BCF), made possible by a P100-million ($2.2 million) grant over three years by the Philippine Council for Industry, Energy and Emerging Technology Research and Development (PCIEERD) of the Department of Science and Technology (DOST).

Dr. Cynthia P. Saloma, Director of the University of the Philippines’ National Institute of Molecular Biology and Biotechnology, and program director of DSCF, said the study of genomics for health and agricultural research is vital in ensuring Philippine competitiveness, especially the local industries.

“For a long time, the Philippines has been very dependent on other countries. We need to send samples to other countries like Australia and Japan because we did not have the infrastructure for research. We realize that it is high time for the government to invest in R&D,” she said.

The DSCF currently offers a full range of DNA sequencing services and provides support for the various programs of the PGC.

“We provide sequencing and genotyping services to academic research groups in the country and the wider scientific community. We also make available our state state-of-the art equipment for the training and manpower development of future genomics researchers in the country,” Saloma said.

Health research

In the area of health research, the DCSF director said as ethnicity plays a key role in disease susceptibility and resistance, there is a need for Filipinized personal medicine through a country-specific database of Filipino genome sequence variations.

This, she said, would be helpful in rapid response to epidemics and pandemics, biogenomic surveillance and forecasting of emerging and re-emerging infections like AH1N1, AHF5N, SARS, and tuberculosis.

“Of course there are data coming from the US, Europe, Japan but there are also a lot of data that cannot just be translated into practices in the Philippines,” she said. “Primarily, there is increasing recognition that ethnicity has a profound role on disease susceptibility. That’s why we need to study the Filipino genome.”

When the PGC was conceptualized in 2009, there were major events in health in the country and in Asia, such as the dengue outbreaks in the Philippines that reached alarming rates, the SARS outbreak in Hong Kong, and the H1N1 outbreak in Mexico, which reinforced the importance of genomics in providing new solutions.

In fact, the first two grants received by the center were for dengue diagnostic testing and H1N1 surveillance.

Investing in next generation sequencing (NGS) equipment capable of high throughput sequencing and genotyping, the current DCSF can provide whole genome sequencing for identifying SNPs, somatic mutations, CNVs and structural variations, as well as targeted re-sequencing and exome sequencing for selected regions.

Saloma said its applications cover in-depth study of specific genes and sequencing assays for diseases.

The center has also been active in the study of genomics for agricultural research. Some of its projects include the coconut genomic program, which include the study of heirloom varieties and biomarker development for fast growth; the genomics of abaca, sugarcane, coffee geared towards improving their productivity; an

In the field of biodiversity and bioenergy, it has undertaken transcriptome sequencing of venom ducts of venomous marine snail for genome-based marine drug discovery, as well as DNA barcoding of birds, fishes and native animals.

Since 2012, a total of more than 100 clients from different sectors of the country have been served by the facility.

High-performance computing

Dr. Arturo O. Lluisma, Program Director, BCF, said extracting information from the genome is the key purpose of DNA/genome sequencing.

“We have to know the sequence and from there hopefully could lead us into an understanding into the genetic causes of observable traits,” he said.

However, this process needs high-performance computing power to analyze this data and transform that data into something useful. The DOST, he said, provides facilities, which include a supercomputer housed at the National Computer Center and large memory servers available at the BCF.

“It is the direction of the DOST to identify core technologies necessary for multi-disciplinary approach to challenges. We are very confident that many of the challenges we face today – effective diagnosis or treatment of diseases and genetic improvement of livestock and crops – can be solved,” said Raymond Liboro, Assistant Secretary, DOST.

The PGC, currently housed at the UP National Institute of Molecular Biology and Biotechnology, will soon move to its own building within the 21-hectare National Science Complex built by the government inside the state university.

Saloma said hopefully this will spur the development of science and technology research, as well as provide incentives for the country’s future researchers to pursue research programs for health and agriculture.