Microarray Core Laboratory

The Microarray Core Laboratory hosts two of the country’s microarray facilities and conducts research services on the ethnic population studies, pharmacogenetics, and the genetic basis of commonly prevalent diseases among Filipinos using high-throughput screening and expression profiling of candidate genes. Completed research involved the identification of some of the variants associated with the following diseases among Filipinos: hypertension, coronary artery disease and myocardial infarction, dyslipidemia, diabetes mellitus, systemic lupus erythematosus, asthma, leptospirosis and sepsis. The laboratory is also actively involved in the translation of the results of these researches into diagnostic or prognostication kits which may help aid clinicians in their care for patients with these diseases.

What is Microarray? Variations in DNA can result in various conditions or phenotypes. Single nucleotide polymorphisms (or SNPs) are sequences that occur when a nucleotide in the DNA differs between paired chromosomes or biological species.

Microarray is a technique used to detect multiple target sequences in an organism’s genome. It can genotype multiple regions in the DNA (deoxyribonucleic acid), can be used to measure expression levels of large number of genes using RNA (ribonucleic acid) simultaneously,  and it can also detect changes in DNA methylation.
These applications can be used to: look for biomarkers associated with certain conditions; seek molecular targets for manipulation; and explain molecular processes related to a trait. 
      
Currently, the Microarray Core Laboratory has on-going programs and projects on the following diseases:
  • Cardiovascular Diseases: 
    • Coronary Artery Diseases
    • Hypertension
    • Dyslipidemia
    • Acute Myocardial Disease
  • Type 2 Diabetes Mellitus
  • Leptospirosis
  • Sepsis
  • Systemic Lupus Erythematosus
  • Asthma
  • COVID-19
The HiScan™ Reader functions as a high-speed, precision imaging scanner for Illumina sequencing and microarray-based analyses. It is a high-resolution optical imaging instrument that uses red and green lasers to detect fluorescence information on BeadChips.  
 
Services offered to research proponents and investigators include:
a.  DNA Extraction  i. DNA Biobanking
b.  PBMC Isolation  j. qPCR
c.  RNA Extraction  k. Serum Separation
d.  RNA Purification    l. miRNA Array
e.  Microarray Custom Genotyping  m. miRNA cDNA
f.   Microarray Whole Genome Genotyping o. miRNA extraction
g.  Microarray Whole Genome Gene Expression p. miRNA PCR Array
h.  DNA Methylation Assay q. ELISA
                   

Ongoing Programs/Projects:

Title: Evaluation of plasma therapy for retarding progression and preventing complications in COVID-19
Investigators: Jose Nevado, Jr., Sullian Naval, Salvador Caoili, Monica Fresthel Climacosa, Ruby Ann King, Pedrito Tagayuna Study period: December 1, 2021 - May 31, 2022
Funder: Philippine Council for Health Research and Development
 
Title: Joint Project For Disease Modelling and Developing Novel Therapeutics: Initial Focus on Acute Myocardial Infarction and Blood Calibration
Investigators: Ahmad Reza Mazahery, Jose B. Nevado Jr., Maria Amelita Estacio, Allan Hilario, Michael Velarde, Elena Catap, Joana Marie Cruz, Aimee Yvonne Criselle Aman, Alexandra Ang
Study period: July 1, 2021 - June 30, 2023
Funder: CHED - Philippine-California Advanced Research Institutes (PCARI)
 

Publications:

Nevado Jr, J. B., & Imasa, M. S. B. (2008). Association of Homocysteine Levels to Traditional Risk Factors in Unstable Angina and Non-ST Elevation Myocardial Infarction: Implications from the FINEST study. Acta Medica Philippina, 42(1).

Nevado Jr, J. B., & Imasa, M. S. B. (2008). Homocysteine predicts adverse clinical outcomes in unstable angina and non-ST elevation myocardial infarction: implications from the folate intervention in non-ST elevation myocardial infarction and unstable angina study. Coronary Artery Disease, 19(3), 153-161.

Imasa, M. S. B., Gomez, N. T., & Nevado Jr, J. B. (2009). Folic acid-based intervention in non-ST elevation acute coronary syndromes. Asian Cardiovascular and Thoracic Annals, 17(1), 13-21.

Cooley, B. C., Nevado, J., Mellad, J., Yang, D., Hilaire, C. S., Negro, A., ... & Boehm, M. (2014). TGF-β signaling mediates endothelial-to-mesenchymal transition (EndMT) during vein graft remodeling. Science Translational Medicine, 6(227), 227ra34-227ra34.

Cutiongco-de la Paz, E. M., Ngelangel, C. A., David-Wang, A., Nevado Jr, J. B., Silao, C. L. T., Hernandez-Sebastian, R., ... & Padilla, C. D. (2017). The Prevalence of CYP2D6 Gene Polymorphisms among Filipinos and their use as Biomarkers for Lung Cancer Risk. Acta Medica Philippina, 51(3).

Albao, D. S., Cutiongco-de la Paz, E. M., Mercado, M. E., Lirio, A., Mariano, M., Kim, S., ... & Seielstad, M. (2019). Methylation changes in the peripheral blood of Filipinos with type 2 diabetes suggest spurious transcription initiation at TXNIP. Human Molecular Genetics, 28(24), 4208-4218. 

Reganit PFM, Nevado Jr. JB, Cutiongco-de la Paz EMC, Taquiso JL, Aman AYCL,…, and Sy RG. (2020). BAG6 Variant rs805303 is Nominally Associated with ACEi-induced Cough Among Filipinos. Philippine Journal of Science, Vol. 149 (1): pp. 35-41. 

Sy RG, Nevado Jr. JB, Llanes EJB, Magno JDA, Ona DID, Aman AYCL,…, and Cutiongco-de la Paz EMC. (2020). The KLOTHO Variant rs36217263 Is Associated With Poor Response to Cardioselective Beta-Blocker Therapy Among Filipinos. Clinical Pharmacology and Therapeutics, Vol. 107(1): pp. 221-226.

Poblete, J. M. S., Ballinger, M. N., Bao, S., Alghothani, M., Nevado Jr, J. B., Eubank, T. D., ... & Magalang, U. J. (2020). Macrophage HIF-1α mediates obesity-related adipose tissue dysfunction via interleukin-1 receptor-associated kinase M. American Journal of Physiology-Endocrinology and Metabolism, 318(5), E689-E700.

Hilario, A. L., Medina, J. R. C., & Nevado Jr, J. B. (2020). Bioinformatic Analysis of Frequently Reported Somatically Mutated Genes of Triple-negative Breast Cancer and Comparison with Top Mutated Genes from the BRCA-UK Project. Philippine Journal of Science, 149(4), 1243-1252.

Santos LG, Nevado JB, Cutiongco-de la Paz EC, Abrahan LL, Aman AYCL,…, and Sy RG. (2021). Variants Near CETP, MTTP and BUD13-ZPR1-APOA5 may be Nominally Associated with Poor Statin Response Among Filipinos. Acta Medica Philippina: Online First. https://actamedicaphilippina.upm.edu.ph/index.php/acta/article/view/2353

Sy RG, Nevado JB, Gonzales EM, Bejarin AP, Aman AYCL,…, and Cutiongco- de la Paz EC. (2021). A Genetic Polymorphism in GCKR may be Associated with Low High-Density Lipoprotein Cholesterol Phenotype among Filipinos: A Case-Control Study. Acta Medica Philippina: Online First. https://actamedicaphilippina.upm.edu.ph/index.php/acta/article/view/2350/.

Runcharoen, C., Fukunaga, K., Sensorn, I., Iemwimangsa, N., Klumsathian, S., Tong, H., ... & Chantratita, W. (2021). Prevalence of pharmacogenomic variants in 100 pharmacogenes among Southeast Asian populations under the collaboration of the Southeast Asian Pharmacogenomics Research Network (SEAPharm). Human Genome Variation, 8(1), 1-6.

Ona DD, Nevado JB, Cutiongco-de la Paz EC, Ramos JD, Aman AYCL, …, and Sy RG. (2021). Variant rs6596140 of Follistatin-like 4 Gene (FSTL4) May Be Associated with Poor Response to Angiotensin Receptor Blockers (ARBs) among Filipinos. Philippine Journal of Science, Vol. 150 (4): pp. 703-21.

Aman AYCL, Sy RG, Nevado JB, Bejarin AP, Reganit PM,…, and Cutiongco-de la Paz EC. (2021). rs17465637 variant of MIA3 may be associated with coronary artery disease among Filipinos. Philippine Journal of Science, Vol. 150 (5): pp. 1051-62.

The Microarray Technology

BeadChips                                          HiScan™ Reader                 
 

      
The HiScan™ Reader functions as a high-speed, precision imaging scanner for Illumina sequencing and microarray-based analyses. It is a high-resolution optical imaging instrument that uses red and green lasers to detect fluorescence information on BeadChips.                                                                                                
 
 
 
 
 

Contact the Microarray Core Laboratory for more information:

The UP-NIH Microarray Core Laboratory
Institute of Human Genetics
The National Institutes of Health
2nd floor, 620 Pedro Gil St., Ermita, Manila 1000
Telephone: 5310-1780 local 116
Email: upnih_microarray@upm.edu.ph