THE PHILIPPINE GENOME CENTER is a multidisciplinary research and service unit of the University of the Philippines for health, agriculture, biodiversity, and the environment. The Center serves as the catalyst for the advancement of genomics research and applications in the Philippines through collaborative intitiatives and multi-sectoral partnerships.
ROAD TO PGC The journey of the Philippine Genome Center is a revelation of teamwork and vibrant spirit instilled by its four founding mothers early on. Despite the pioneering challenges, the Center which literally began as a virtual research unit, continue to work hard in realizing its mandate and goals to liven up a reliant R&D community.
10 YEARS
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On behalf of the Department of Science and Technology (DOST), I would like congratulate the Philippine Genome Center (PGC) for the conduct of the 1st National Genomics Conference! With the theme “Omics research in the next 5 years with the Philippine Genome Center”, the conference aims to showcase the research programs of PGC to help strengthen research studies in health, agriculture, biodiversity, and the environment through utilizing the omics field of study. It is hoped that this conference brings together a network of investigators, researchers, research organizations, and the academe to improve our existing research collaborations.
MESSAGES
To all the participants, may you take this opportunity to share knowledge and gain new insights in omics research. The DOST commends the PGC for its dedication in furthering scientific development in the country, and for bringing science closer to the Filipino people.
Fortunato T. De La Peña Secretary Department of Science and Technology
Congratulations to the Philippine Genome Center on its conduct of the 1st National Genomics Conference! The University lauds the efforts of PGC to continuously bring its expertise and services to the wider public through programs such as this conference. Anchored on the noble vision of being “a center of excellence in gene discovery and genomics research that effectively translates knowledge into applications beneficial to the Philippine society,� PGC pursues knowledge crucial to our understanding of who we are as a people and how we relate to the rest of world. It undertakes research activities that are critical to solving many problems in health and medicine, agriculture, biodiversity, forensics and ethnicity, industry, and the environment. The work of PGC goes beyond the confines of UP. It reaches out to stakeholders so they may become our partners in scientific investigations, discoveries, and breakthroughs. Collaboration lies at the heart of PGC. This is a commitment to promote, disseminate, and encourage participation and cooperation so that the overarching goals of deepening our understanding of genomics and bioinformatics and judiciously applying advanced knowledge and emerging technologies may be accomplished to benefit all of humanity. To all principal investigators and researchers participating in this conference, UP takes great pride in your work. Maraming salamat sa inyong ambag sa larangan ng genomics at bioinformatics!
Danilo L. Concepcion President University of the Philippines
As the national university, UP is extremely privileged to host the Philippine Genome Center (PGC). Drawing on the strengths of the different UP campuses, the Center has been at the forefront of world-class genomics research and bioinformatics in the Philippines, addressing for 10 years now the country’s major challenges in health, agriculture, biodiversity and the environment. We had repeatedly reminded our colleagues in PGC that the Center, while lodged in UP, has a mission that goes beyond the University. Its shared core research facilities for instance help scientists in and outside UP advance research that could eventually translate into innovations and technologies for the well-being of our people. Its capacity building programs have been contributing to an expanded pool of genomics researchers while its immersion activities for high school students promise to attract them to disciplines that would open the field of genomics research for them in the future. I applaud the PGC Team for organizing this 1st genomics conference that aims to empower researchers nationwide. May the Team and PGC move from strength to strength! Padayon, UP!
Maria Cynthia Rose Banzon Bautista, PhD Vice President for Academic Affairs University of the Philippines
Congratulations to the Philippine Genome Center (PGC) for the conduct of the 1st National Genomics Conference! Since its establishment in 2009, the PGC has achieved a number of significant achievements. From capacity building of experts and future scientists/researchers in the field of genomics and bioinformatics to the expansion of its reach to Visayas and Mindanao, the PGC is widening the country’s opportunity to become a leader in genomics research. This Conference will encourage more collaborations from various stakeholders - from the academe, government and the private sector as well - to spearhead our venture into strengthening the genomics research infrastructure of the country. I hope that industry engagement will significantly increase in the coming years, there will be more technologies transferred, and Genomics will be mainstream in many of our academic institutions and research institutions. Again, congratulations and keep up the good work!
Rowena Cristina L. Guevara, PhD Undersecretary for Research and Development Department of Science and Technology
On behalf of the Department of Science and Technology— Philippine Council for Health Research and Development (DOST-PCHRD), I would like to extend my warmest congratulations to the Philippine Genome Center (PGC) for holding the 1st National Genomics Conference! Since the establishment of the Philippine Genome Center, omics research has progressed. In health, the DOST-PCHRD supported the development of diagnostic devices and personalized treatments for diabetes and cardiovascular diseases (CVDs). We recognize also that PGC’s partnership with the Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development (PCAARRD) generated innovation in agriculture through the development of genetically-improved crops. While we see PGC’s initial work in health and agriculture, we believe that other sectors will benefit from genomics research. With the theme, “Omics research in the next 5 years with the Philippine Genome Center,” we hope that this gathering will lead us to more collaborations that will generate innovations for healthier communities, making our lives better. Mabuhay ang Philippine Genome Center!
Jaime C. Montoya, MD, MSc, PhD, CESO III Executive Director Philippine Council for Health Research and Development Department of Science and Technology
Greetings! Six years from the launching of the Philippine Genome Center (PGC)-DNA Sequencing Core Facility, our researchers, experts in the field of biotechnology, genomics and related fields are now together for this 1st National Genomics Conference to present their valuable outputs from the researches that were accomplished through the PGC. Before the PGC, only a handful of genomic researches were undertaken since sending samples abroad were not only time-consuming but also very expensive. Now, because of the unmatched dedication and commitment of our researchers and with funding support from the government, particularly the DOST and its agencies, this event has come to fruition. On behalf of PCIEERD, I would like to congratulate the Organizers and wish this conference a great success.
Enrico C. Paringit, PhD Executive Director Philippine Council for Industry, Energy and Emerging Technology Research and Development Department of Science and Technology
Warm greetings to the organizers, participants and guests of the “1st National Genomics Conference!” The conference with the theme: Omics Research in the Next Five Years with the Philippine Genome Center” highlights the accomplishments of the center as well as its commitment to translate genomic research and discoveries into applications beneficial to the Filipino people. I commend the Philippine Genome Center on its efforts to support the agriculture, aquatic and natural resources(AANR) sector by nurturing the country’s promising genomic scientists, researchers and experts and providing them access to state-of-the-art facilities. To the genomic scientists, researchers and experts, thank you for sharing your valuable knowledge and expertise. May you continue to thrive and work together in addressing relevant issues and concerns. I am confident that this conference will foster collaborations and form linkages among researchers and ultimately contribute to national development and progress. Mabuhay!
Reynaldo V. Ebora, PhD Executive Director Philippine Council for Agriculture, Aquatic and Natural Resources Research and Development Department of Science and Technology
“We are here to collaborate and to be of service to research organizations and academic institutions in their advanced research using Next Generation Sequencing and bioinformatics” The 1st National Genomics Conference themed “Omics research in the next 5 years with the Philippine Genome Center” was conceptualized to bring together principal investigators, decision-makers, and academic mentors from Luzon, Visayas, and Mindanao. Envisioning an increase in research collaborations, the Philippine Genome Center is showcasing some of its completed and ongoing research endeavors to provide ideas and inspiration that could serve as our take off points for our discussions to collaborate. As the Center marks its 10th year in UP, we aptly themed and focused this conference on “omics” research because we have an array of tools and equipment units to aid researchers in their genomics, proteomics, transcriptomics, metabolomics and/or bioinformatics endeavors. These would enable us to look at problems and find solutions to them in a multi-omics approach that would significantly add depth and scope into our analysis. This conference, similar to most of the events we organize, is anchored on multidisciplinary cooperation and fusion of expertise for a common good. We at the PGC are committed towards providing an avenue by which research experts from different fields are able to work together on research projects that will prove meaningful and useful to Filipinos. I am pleased to share as well that this event is the first of ten (10) stakeholder engagement activities we are rolling out to scale up collaboration in health, agriculture, biodiversity and environment-focused research. Be it in Luzon, Visayas, or Mindanao, the PGC welcomes you, and it is our wish that through our various activities, we help empower the scientific endeavors of our local researchers and students through research and academic partnerships. Thank you and we look forward to working with you!
Cynthia P. Saloma, PhD Executive Director Philippine Genome Center
TALKS Keynote Speaker: Asao Fujiyama, PhD
01
Coconut Genetics and Genomics in the Philippines: Updates and Opportunities Towards a Vibrant Coconut Industry Hayde Flandez-Galvez, PhD
02
The Conus Exogenomics Program Arturo Lluisma, PhD
03
Saktong Lunas para sa Puso ng Pilipino Rody G. Sy, MD
04
Genomic Association Studies in Filipinos on Treatment, Diagnosis and Risk Assessment of Type 2 Diabetes Mellitus and Its Related Medical Condition Eva Cutiongco-dela Paz, MD
05
Novel mutations in EGFR pathway genes of Filipino colorectal cancer patients present distinct and overlapping oncogenic phenotypes Reynaldo L. Garcia, PhD, MPhil (cantab)
06
Four Areas in which Genomics is Driving Precision Health Renee Gallagher
07
Precision Medicine Initiative: From Science to Clinical Toh Wen Hong, PhD
08
Program Management Coordination Project Cynthia P. Saloma, PhD
09
Establishment of PGC in Mindanao Lyre Murao, PhD
10
Establishment of PGC in Visayas Victor Marco Emmanuel Ferriols, PhD
11
The Protein, Proteomics and Metabolomics Facility at PGC: Probing the Functional Significance of Genomic Potential Neil Andrew D. Bascos, PhD
12
Developing a Laboratory Information Management System (LIMS) for Biorepository Facility Elena S. Catap, PhD
COCONUT GENETICS AND GENOMICS IN THE PHILIPPINES: UPDATES AND OPPORTUNITIES TOWARDS A VIBRANT COCONUT INDUSTRY
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ABSTRACT
Hayde Flandez-Galvez, PhD
The Philippines is the second world supplier of coconut by-products. Used to be the topmost producer/supplier, the country however has been threatened with drastic production constraints such as agro-climatic and weather calamities, farm devastations by disease/insect pest outbreak, and spreading existence of non-bearing and senile palms in coconut plantations. To facilitate the development of resilient and outstanding varieties especially for added high-value traits, the advancement in genomics and related technologies are harnessed for their optimum integration in the coconut breeding program. Coconut whole genome sequence reads were generated using ‘Catigan Green Dwarf’ (CATD) as the reference variety and combinations of advanced next generation sequencing (NGS) platforms. High quality genome assembly was generated and used to characterize adaptation and economically important genes i.e. candidate resistance genes, drought tolerance, productivity, and coconut oil related genes. Genome-wide and gene specific DNA markers are generated. A user-friendly database is being developed to house the coconut genome sequence data, gene/trait models and associated DNA markers for access by all coconut researchers – students, experts, and basic and applied researches alike. Updates including challenges encountered will be presented on the specific applications of the output from the coconut genomics project. These include gene mining for host resistance against coconut scale insect (CSI) and screening for CSI least damaged coconut varieties, as well as characterization of coconut genes related to ‘Makapuno’, ‘Lono’ and coconut oil qualitative/quantitative traits. Significant result from initial molecular and biochemical studies that support nutritional and medicinal claims will also be presented. The unprecedented opportunities beyond basic science from these major S&T achievements in coconut and in integration with applicable new breeding technologies will be discussed.
THE CONUS EXOGENOMICS PROGRAM
ABSTRACT
Arturo Lluisma, PhD
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Conopeptides found in the venom of Conus species can function as ligands, and thus as agonists or antagonists, of a variety of ion channels in human neuronal membranes. Their significant biomedical potential makes them important targets of drug discovery efforts. Because these peptides are encoded in Conus genomes, high-throughput DNA sequencing technologies can be leveraged for their discovery. The challenge now is how to exploit the wealth of primary structure data to facilitate the determination of their function and the realization of their therapeutic potential. Although experimental approaches will continue to be essential in the determination of the structure and function of conopeptides, in-silico approaches will be key to accelerating the discovery process. Advances in computational technologies (hardware and software as well as modelling and machine learning algorithms) have made it possible to predict structural and functional characteristics of peptides in silico at a useful level of accuracy. Exploiting these technologies, the Conus Exogenomics Project funded by the UP EIDR Program has initiated the development of a computational framework that will enable high-accuracy prediction of the 3D structure of conopeptides as well as their target receptors. The first tool developed made use of machine learning techniques to infer the most likely target membrane receptors of these peptides given their amino acid sequences. Further work is underway to build higher-quality training data sets and to explore other computational techniques that could potentially yield better predictions. The tools that will be developed are expected to significantly facilitate the identification, in a high-throughput fashion, of receptors for a large number of uncharacterized or novel conopeptides emerging from transcriptomics-based workflows.
SAKTONG LUNAS PARA SA PUSO NG PILIPINO
ABSTRACT
Rody G. Sy, MD
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Cardiovascular disease is the leading cause of death among Filipinos. Risk factors like smoking and obesity are known to contribute to the development of cardiovascular diseases, but studies show that genetics also play a role. There are available drugs to address these, but drugs do not work the same way for everyone, which is also partly due to differences in genetic makeup of patients. Although there are genetic markers associated with cardiovascular diseases and responses to cardiovascular drugs among different populations, Filipino-specific researches need to be done because of differences in the genetic makeup of different ethnicities, and there is an underrepresentation of Filipinos in studies conducted abroad. We enrolled 2,320 adult Filipinos with high blood pressure, high blood cholesterol, heart attack and stroke to determine whether genetic variants called single nucleotide polymorphisms are associated with increased risk to develop cardiovascular diseases. We also examined if the variants are related to how Filipinos respond to the drugs that we take for these diseases. The group has determined some variants associated with the development of cardiovascular diseases and poor response to different cardiovascular medications among Filipinos. These variants may be used as potential biomarkers in genetic test kits appropriate to our local setting for early diagnosis of cardiovascular diseases, and to aid doctors and patients in choosing the best drugs compatible with their genetic makeup. These variants will also contribute to the knowledge on the different mechanisms of how these diseases develop. Physicians may find it useful to possibly include genetic testing in future clinical practice guidelines for cardiovascular diseases, after further researches on the efficacy of genetic tests and economic evaluation of the value of including genetic testing in standard cardiovascular healthcare, realizing the goal of “saktong lunas para sa Pilipino�.
GENOMIC ASSOCIATION STUDIES IN FILIPINOS ON TREATMENT, DIAGNOSIS AND RISK ASSESSMENT OF TYPE 2 DIABETES MELLITUS AND ITS RELATED MEDICAL CONDITION
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ABSTRACT
Eva Maria Cutiongco-de la Paz, MD Elizabeth Paz-Pacheco, MD Jose Nevado, MD, PhD
Type 2 Diabetes Mellitus (T2DM) is the 6th leading cause of death among Filipinos and there are over 3.5 million Filipinos diagnosed to have this condition. It remains as a major cause of mortality and morbidity attributed to its long-term complications. There is growing evidence to support that there are genetic variants that can be used as biomarkers for susceptibility to T2DM as well treatment responses to oral anti-diabetic agents. However, there is a lack of proper diagnostic methods for prediction of disease susceptibility, drug response and complications of T2DM. Identifying genetic biomarkers can help elucidate the disease further. The program has three major components. The first is the evaluation of candidate genetic variants as pharmacogenetics markers for commonly used oral hypoglycemic agents. The aim of this project is to determine the genetic polymorphisms associated with drug response to metformin, gliclazide and glimepiride in type 2 diabetes mellitus (T2DM). The second project is the correlation of candidate genetic variations for susceptibility and risk assessment of type 2 diabetes mellitus among Filipinos, This project aims to determine genetic variants associated with type 2 diabetes mellitus (T2DM) that can help in the development of personalized care for Filipinos. The third project is the differential gene expression and pathway analysis of type 2 diabetes mellitus comorbidities in the Filipino population. The aim of this project is to identify in T2DM Filipinos with vascular complications differentially expressed genes and understand their pathway mechanisms which may pose as possible biomarkers from resulting gene expression profiles. Genetic studies for T2DM opens the opportunity to address the need to optimize T2DM management and individualize treatment for Filipinos. Funded by the Philippine Council for Health Research and Development, Department of Science and Technology
NOVEL MUTATIONS IN EGFR PATHWAY GENES OF FILIPINO COLORECTAL CANCER PATIENTS PRESENT DISTINCT AND OVERLAPPING ONCOGENIC PHENOTYPES
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ABSTRACT
Reynaldo L. Garcia, PhD, MPhil (cantab) Krizelle Mae Alcantara Joshua Reginald Malapit Ryan Timothy Yu Jose Antonio Ma. Garrido John Paul Rigor Kevin Kent Vincent Canlas Arlou Kristina Angeles Eva Maria Cutiongco Dela Paz, MD
Colorectal cancer (CRC) ranks as the fourth most common cancer in the Philippines and has overtaken liver cancer as the number one gastro-intestinal malignancy. An established druggable target for monoclonal antibody-based therapeutics is the epidermal growth factor receptor (EGFR), which is often overexpressed in CRC. Until recently, KRAS status (wild type or mutated in hotspot codons) was used as the sole predictive marker for therapeutic response. There is consensus, however, that uncharted mutations including genetic lesions in the NRAS isoform and in effectors downstream of KRAS, should be investigated in patients with wild-type KRAS allele but are refractory to anti-EGFR therapy. Advances in next generation sequencing (NGS) have expanded our view of the mutational landscape of CRC throughout the progression of the disease, and the extent of tumor heterogeneity. Here, we present the identification and phenotypic characterization of 14 novel and non-hotspot mutations in the KRAS, NRAS, BRAF, PIK3CA and PTEN genes from 90 Filipino CRC patients. The mutants were analyzed for their effects on cellular proliferation, resistance to apoptosis, cytoskeletal reorganization, and migratory capacity. Results show overlapping and distinct oncogenic readouts among the mutants. Elucidation of differential effector engagement responsible for the different phenotypes observed will be instructive; and if validated in in vivo mouse studies, 3-dimensional cell cultures, and clinical correlates, these can have wide implications in choosing treatment options. Additionally, we identified microRNA response element (MRE) single nucleotide polymorphisms in the 3’UTR of the five genes of all 90 patients and present here the in silico analysis of likely effects on miRNA binding and MRE occupancy as well as target protein levels, function and/or dysregulation.
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FOUR AREAS IN WHICH GENOMICS IS DRIVING PRECISION HEALTH
ABSTRACT
RenĂŠe Gallagher
Adoption of genomics-powered precision health is prevalent across four areas in healthcare. These areas include Rare and Undiagnosed Genetic Diseases (RUGD), Precision Oncology, Pharmacogenetics and Applied Microbiology and Metagenomics. Medicine is shifting from the intuitive, symptom based, trial-and-error therapies of today, to the provision of care targeting the underlying biology with predictable effective treatments. This paradigm shift for application of genomics in a multitude of settings is driving the further implementation and integration of precision health into routine healthcare.
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INITIATIVE: FROM SCIENCE TO CLINICAL OUTCOME
ABSTRACT
Toh Wen Hong, PhD
Globally, many large scale population genomics initiatives are taking place. This is stemmed from the belief that current procedure of one size fit all medical treatment is not the most effective approach. Rather the new belief is that healthcare should be customized for each individual. This approach relies on mapping of the genetic and/or multi-omics diversity of each population to the phenotype outcomes. The hope is that customized healthcare can then be targeted to individual profiles to improve population health. In this short talk, I would like to share with you how Thermo Fisher Scientific can be your valuable partner as you venture along this exciting journey.
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PROGRAM MANAGEMENT COORDINATION
ABSTRACT
Cynthia P. Saloma, PhD
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The Program Management Coordination (PMC) Project offers the necessary support for the proposed expansion activities of the Philippine Genome Center’s satellite operations in the Visayas and Mindanao. Significant events include the completion and operational maintenance of their core facilities and securing signatories and affiliates for the nationwide genomics consortia. To continuously promote high levels of trust and collaboration among the different project teams, we have created clear and delineated channels of communication. In doing so, we have generated and shared the standard operating procedure (SOP) in PGC-affiliated’ omics research proposals and various marketing and branding collaterals as part of our first-year accomplishments. As a result of our collaborative discussion during NSTW, we have also outlined both the unifying and distinctive features of the different regional PGC programs to be integrated into the production of graphic materials and event collaterals. The project also served as a conduit for forming institutional linkages to build and submit program-level genomics research proposals in medicine and public health, agriculture, livestock, fisheries, forestry, biodiversity, and ethnicity. These are all part of DOST’s strategic mandate to strengthen research infrastructure and capacity. We planned and initiated different touchpoint meetings outside of Manila to cultivate strong partnerships with potential collaborators. The PMC project remains mindful of its role in propagating innovative knowledge-sharing methods to ensure the attainment of Visayas and Mindanao project goals. Today, we have invited representatives from different SUCs, HEIs, private entities, and other public agencies involved and interested in genomic research. They are here to witness and take part in the culmination of the ten-year journey of establishing the Philippine Genome Center.
ESTABLISHMENT OF THE PHILIPPINE GENOME CENTER IN MINDANAO
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ABSTRACT
Lyre Anni Espada-Murao, PhD
Mindanao is one of the last frontiers of Philippine biodiversity and has the largest concentration of ethnic minorities in the country. Its fertile soil and rich bioresources supports the bulk of Philippine agriculture, while much of its other resources have yet to be explored. The colorful ethnic background of its people, coupled with migrants from the mid-20th century onwards, has expanded cultural and human diversity. Its unique social and biological ecosystem confers Mindanao with an immense potential for research and development that makes it an exciting ground for new discoveries and innovations. Omics is a promising technology that can facilitate such initiatives at an advanced pace through its high throughput strategy. With the recent establishment of the Philippine Genome Center Mindanao Satellite Facility (PGC MSF), omics research is now within closer reach to the Mindanao community. The first and one of its kind in the Island, PGC MSF will soon operate with a state-of-the-art omics facility in cooperation with the headquarter facility in UP Diliman to bolster research capacity and output in Mindanao and make services and trainings available and accessible to the region. Key to this is the establishment of the Mindanao Genomics Consortium, a body of local stakeholders who will support and propagate omics-based R&D. In its first year of operation, PGC MSF has embarked on a series of networking and promotional activities which were received with enthusiasm, signifying that the region is ripe for omics. This is anticipated to open doors for exploring opportunities, challenges, and issues relevant to Mindanao. By facilitating science for Mindanao by Mindanaoans, PGC MSF therefore intends to be a catalyst for growth and development in the region.
ESTABLISHMENT OF THE PHILIPPINE GENOME CENTER IN VISAYAS
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ABSTRACT
Victor Marco Emmanuel N. Ferriols, Ph.D.
The expansion of the Philippine Genome Center towards other regions is viewed as a timely and much needed initiative, not only to boost the research capabilities of these regions but to further spur regional development through the utilization of the latest advances in omics and bioinformatics. Through the efforts of the Philippine Genome Center Visayas Satellite Facility (PGC VSF), the Visayas Genomics Consortium has taken shape with stakeholders coming from various state universities and colleges, higher education institutions, health facilities, government agencies, and other research institutions. To date, the consortium is composed of more than 20 members coming from Regions VI, VII, and VIII of the Visayas as well as several partners from beyond these regions. With an initial focus on fisheries and aquatic resources as the core strength of PGC VSF, consortium members have started formulating research proposals on the utilization of omics for commodity improvement and conservation strategies for marine and freshwater ecosystems. PGC VSF has also taken the lead in encouraging medical doctors within the region in tapping genomics as a tool to enhance their research initiatives. Current and future programs of PGF VSF will be discussed during this talk.
THE PROTEIN, PROTEOMICS AND METABOLOMICS FACILITY AT PGC: PROBING THE FUNCTIONAL SIGNIFICANCE OF GENOMIC POTENTIAL
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ABSTRACT
Neil Andrew D. Bascos PhD
The establishment of the Philippine Genome Center has paved the way for Omics research in the Philippines, greatly benefiting the health, agricultural, and industrial sectors. In particular, the core facilities of the PGC has provided several pioneering projects that laid the proper infrastructure for the investigation of available genomic information. Now, the PGC aims to bring Philippine Omics research to greater heights by improving its facilities to analyze proteomes and metabolomes through the establishment of the Protein, Proteomics and Metabolomics (PPM) Facility. Proteomic analysis will enable direct assessment of protein expression, which allows the elucidation of key components for desired traits and specialized functions. On the other hand, metabolomic analysis will enable the detection of aberrant cellular processes through the use of metabolic products as biomarkers for altered states. These improvements will complement the existing facilities of the PGC by validating predictions from genome-based analyses to test their functional significance in the tested samples. Through its services the PPMF aims to support the health, agriculture, forensics and ethnicity, and biodiversity programs of the Philippine Genome Center and other clients in the public and private sectors. In particular it aims to facilitate the discovery and use of functional molecules of biological and biomedical importance and the development of innovative therapeutic strategies and technologies. Through its promotion of cross-disciplinary research the PPMF aims to train and produce competent and innovative researchers from all over the country, equipped with skills in the use of Omics level technologies, for the advancement of scientific discovery and enterprise.
DEVELOPING A LABORATORY INFORMATION MANAGEMENT SYSTEM (LIMS) FOR BIOREPOSITORY FACILITY
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ABSTRACT
Elena S. Catap, PhD Jan Michael C. Yap, PhD
The successful mapping of the human genome in 2003 significantly enhanced scientific advancement through genomics. This led to the development of large genomic data sets and brought us to the “Era of Big Data”, where large genomic information is required to acquire significant data for basic, applied, and translational research. To support these research endeavors, resource centers such as biobanks and biorepositories are currently given great importance. These facilities foster research by providing storage and accessibility of biospecimens along with its associated information. Although more specimens and data are being produced, a common gap that limits researchers in efficient data gathering is the accessing of data from diverse sources. In the Philippines, the establishment of the Philippine Genome Center (PGC) Biorepository Core Facility, is envisioned to aid various research institutions by providing a systematic and regulated storage of DNA, RNA, cells, tissues, blood and/or other body fluids, and its associated data. To accomplish this goal, a laboratory information management system (LIMS) will also be created. The creation of LIMS will allow efficient tracking of samples and big data generated by various research programs. This will be accomplished by linking sample collection by various research studies, sample processing by “omics” researchers, and sample storage and distribution. The LIMS project will provide the infrastructure on data management workflow to allow the integration of existing PGC laboratory and research databases as well as the development of standard protocols and operational policies on samples to be biobanked.
PGC SERVICES DNA Sequencing Core Facility (DSCF) ATG C TG ACTCCA C ATC GATG GA G G A A T G T A AG A A T C G A T GC G GA ATG C T A AT G GTA GA ATC G
Identifying appropriate sequencing strategies to efficiently meet research goals. DSCF offers a full range of DNA sequencing services from single gene sequencing of capillary sequencers to medium and high-throughput sequencing of Illumina, Ion Torrent and PacBio platforms. It is a central facility that accepts sequencing service requests from clients, conducts quality control tests, analysis and characterization to samples, and provides consultation on the selection of technology platforms in the most costeffective, reliable and efficient way possible. Funded by the Department of Science and Technology (DOST) - Philippine Council for Industry, Energy, and Emerging Technology Research and Development (PCIEERD), DSCF was integrated to the day-to-day operations of the University’s Philippine Genome Center by late 2013. Both the DNA Sequencing Core Facility and the Core Facility for Bioinformatics began offering laboratory atnd technical services pertinent to genomics and bioinformatics research.
Core Facility for Bioinformatics (CFB) A suite of Bioinformatics services from scripting to full project workflows. CFB pursues research programs that are relevant to PGC’s thrusts, including the development of novel or improved computational techniques (i.e. algorithms) and tools (i.e., software), as well as collaborative research projects that aim to find solutions to complex and computing-intensive problems. The core facility also provides data processing and analytical services for clients wishing to outsource data analysis for their nextgeneration sequencing data, and make available high-performance computing servers for clients who wish to do their own data analysis. CFB started as a capability-building project funded by the Department of Science and Technology (DOST) - Philippine Council for Industry, Energy and Emerging Technology Research and Development (PCIEERD). As the project ended in 2014, the core facility was integrated to the day-today operations of the Philippine Genome Center servicing researchers and students in Next Generation Sequence (NGS) data analysis, providing technical support, and giving training courses to further increase local competency in bioinformatics.
The Bioinformatics Training and Internship Program, expanded thanks to a grant by the Department of Science and Technology, is a 6-week program that provides interns with an opportunity to hone and develop their bioinformatics knowledge and practical skills in a collaborative and multidisciplinary environment. In 2019, the Core Facility for Bioinformatics welcomed students and young professionals in biology, molecular biology, mathematics, statistics, computer science, and related fields, particularly those who are keen on pursuing research careers in bioinformatics and computational biology. Accepted applicants will receive training in introductory biology, genomics, and bioinformatics; and will be working on projects related to research or infrastructure development in bioinformatics or computational biology.
PHILIPPINE GENOME CENTER
EXECUTIVE COMMITTEE Danilo L. Concepcion President University of the Philippines
Maria Cynthia Rose Banzon Bautista, PhD Vice President for Academic Affairs University of the Philippines
Cynthia P. Saloma, PhD Executive Director
Raul V. Destura, MD, MBA, FPSMID Deputy Executive Director
Eva Cutiongco-Dela Paz, MD Program Director Health Program
Antonio C. Laurena, PhD Program Director Agriculture, Livestock, Fisheries, and Forestry Program
Ian Kendrich C. Fontanilla, PhD Program Director Biodiversity, Ethnicity and Forensics Program
Jan Michael C. Yap, PhD Program Director Computational Genomics and Systems Biology Program
Benedict A. Maralit, PhD Program Director DNA Sequencing Core Facility
Elena S. Catap, PhD Program Director Biobank Core Facility
Neil Andrew D. Bascos, PhD Program Director Protein, Proteomics and Metabolomics Facility
Victor Marco Emmanuel N. Ferriols, PhD Program Director PGC Visayas Satellite Facility
Lyre Anni Espada-Murao, PhD Program Director PGC Mindanao Satellite Facility