Creating a Roadmap for Building a Sustainable Genomics Facility in the Philippines
Alexander T. Young*
Philippine Genome Center
University of the Philippines Diliman, Quezon City 1101 Philippines
Genomics, bioinformatics, and high-throughput technologies provide a means to create breakthrough solutions for a remarkably wide diversity of fields – including medicine, agriculture, fisheries, livestock, and biodiversity. Significantly, the precision of genomics and DNA enable the creation of applications that are specifically optimized for the Philippines. Dissemination of these technologies throughout the country is accelerated by genomics facilities that provide access to core technologies. However, there are significant scientific and business challenges for creating a sustainable genomics facility in the Philippines. The historical successes and challenges of genomics and high-throughput technologies are reviewed, which point to potential solutions for creating a sustainable genomics facility in the Philippines.
New and exciting advances in genomics and high-throughput technologies are revolutionizing the application of biological sciences. Advances in engineering, microfluidics, robotics, and miniaturization have created machines that can rapidly determine the DNA sequence of an organism’s genes or the entire genome. Similar advances in miniaturization have created machines that can rapidly test the activity of thousands of biological samples (high-throughput assays). High-throughput assays can be used to screen libraries of thousands of chemical compounds for the identification of new drug molecules that combat disease (high-throughput screening). Technologies that simultaneously profile thousands of RNA transcripts to measure gene activity (transcriptomics), proteins (proteomics), metabolites (metabolomics), and microorganisms (microbial community profiling/metagenomics) in response to disease, drugs, or the environment promise to unravel the complexities of biological systems in order to find new applications that benefit society. In conjunction with the technological advances in biology and engineering, advances in computational sciences have enabled the daunting task of interpreting the massive amounts of data that these technologies generate (bioinformatics). The ability to profile thousands to millions of biological molecules in a massively parallel fashion promises to create new biological insights that can lead to better medicines, agriculture, fisheries, forensics, and molecular diagnostics. All of these new technologies are available or being developed at the Philippine Genome Center (PGC). . . . read more
BISHOP JM, VARMUS HE. 2019. The Nobel Prize in Physiology or Medicine 1989. Stockholm: Nobel Media AB. Retrieved from https://www.nobelprize.org/prizes/medicine/1989/summary/ on 15 Mar 2019.
[BFAR] Bureau of Fisheries and Aquatic Resources. 1997. Philippine profile: Department of Agriculture – Bureau of Fisheries and Aquatic Resources, Manila. Retrieved from https://www.bfar.da.gov.ph/publications.jsp?id=29#post on 15 Mar 2019.
[BFAR] Bureau of Fisheries and Aquatic Resources. 2019. Average weekly prices (per kilo) of fresh fish commodities monitored in Luzon (for December 2018 Region IV-B). Retrievd from https://www.bfar.da.gov.ph/files/img/photos/Luzon.1.4.15.pdf
BRUNO JF, SELIG ER. 2007. Regional decline of coral cover in the Indo-Pacific: Timing, extent, and subregional comparisons. PLOS One 2(8): 711.
CARPENTER KE, ABRAR M, AEBY G, ARONSON RB, BANKS S, BRUCKNER A, CHIRIBOGA A, CORTÉS J, DELBEEK JC, DEVANTIER L, EDGAR GJ, EDWARDS AJ, FENNER D, GUZMÁN HM, HOEKSEMA BW, HODGSON G, JOHAN O, LICUANAN WY, LIVINGSTONE SR, LOVELL ER, MOORE JA, OBURA DO, OCHAVILLO D, POLIDORO BA, PRECHT WF, QUIBILAN MC, REBOTON C, RICHARDS ZT, ROGERS AD, SANCIANGCO J, SHEPPARD A, SHEPPARD C, SMITH J, STUART S, TURAK E, VERON JE, WALLACE C, WEIL E, WOOD E. 2008. One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Science 321: 560–563.
CASKEY CT. 1997. Sequence to function in mammals. Second Annual Conference on Functional Genomics; IBC, San Diego, CA.
COUDRAY N , OCAMPO PS, SAKELLAROPOULOS T, NARULA N, SNUDERL M, FENYO D, MOREIRA AL, RAZAVIAN N, TSIRIGOS A. 2018. Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning. Nature Medicine 24: 1559–1567.
EZKURDIA L, JUAN D, RODRIGUEZ JM, FRANKISH A, DIEKHANS M, HARROW J, VAZQUEZ J, VALENCIA A, TRESS ML. 2014. Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes. Human Molecular Genetics 23(22): 5866–5878.
[FDA] Food and Drug Administration. 2018a. Table of Pharmacogenomic Biomarkers in Drug Labeling. Silver Spring, MD: Department of Health and Human Services. Retrieved from https://www.fda.gov/drugs/scienceresearch/ucm572698.htm on 15 Mar 2019.
[FDA] Food and Drug Administration. 2018b. Novel Drug Approvals for 2017. Silver Spring, MD: Department of Health and Human Services. Retrieved from https://www.fda.gov/drugs/developmentapprovalprocess/druginnovation/ucm537040.htm on 15 Mar 2019.
[JICA] Japan International Cooperation Agency. 2015. JICA, Japanese, Filipino scientists’ project backs conservation of ‘highly endangered’ Boracay ecosystem [Press release dated 28 May 2015].
KAMB A. 2005. What's wrong with our cancer models? Nature Reviews Drug Discovery 4: 161–165.
MCCOUCH SR, WRIGHT MH, TUNG CW, MARON LG, MCNALLY KL, FITZGERALD M, SINGH N, DECLERCK G, AGOSTO-PEREZ F, KORNILIEV P, GREENBERG AJ, NAREDO MEB, MERCADO SMQ, HARRINGTON SE, SHI Y, BRANCHINI DA, KUSER-FALCA PR, LEUNG H, EBANA K, YANO M, EIZENGA G, MCCLUNG A, MEZEY J. 2016. Open access resources for genome-wide association mapping in rice. Nature Communications 7: 10532.
MED AD NEWS. 1999. The top 500 prescription drugs by worldwide sales. p. 10–15.
[NIH] National Library of Medicine. 2018. Effect of Dalcetrapib vs. Placebo on CV Risk in a Genetically Defined Population with a Recent ACS (dal-GenE) [Identifier NCT02525939]. Bethesda, MD: National Institutes of Health. Retrieved from https://clinicaltrials.gov/ct2/show/NCT02525939?term=dal-genE&rank=1 on 15 Mar 2019.
RUEDA OM, SAMMUT SJ, SEOANE JA, CHIN SF, CASWELL-JIN JL, CALLARI M, BATRA R, PEREIRA B, BRUNA A, ALI HR, PROVENZANO E, LIU B, M PARISIEN, GILLETT C, MCKINNEY S, GREEN AR, MURPHY L, PURUSHOTHAM A, ELLIS IO, PHAROAH PD, RUEDA C, APARICIO S, CALDAS C, CURTIS C. 2019. Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups. Nature 567: 399–404. doi: 10.1038/s41586-019-1007-8
OVERINGTON JP, AL-LAZIKANI B, HOPKINS AL. 2006. How many drug targets are there? Nature Reviews Drug Discovery 5(12): 993–996.
PFEFFER MA, DUBE MP, TARDIF JC. 2018. Randomized Clinical Trial Needed to Confirm Whether Dalcetrapib Improves Outcomes for Specific ADCY9 Genotype. JAMA Cardiology 3(9): 897. doi: 10.1001/jamacardio.2018.2379
PHILIPPIDIS A. 2018. The top 15 best-selling drugs of 2017. Genetic Engineering & Biotechnology News. Retrieved from www.genengnews.com/a-lists/the-top-15-best-selling-drugs-of-2017/
[PSA] Philippine Statistics Authority. 2019. Updates on palay, rice and corn prices (third week of January 2019). Retrieved from https://psa.gov.ph/content/updates-palay-rice-and-corn-prices-0
PUSHPAKOM S, IORIO F, EYERS PA, ESCOTT KJ, HOPPER S, WELLS A, DOIG A, GUILLIAMS T, LATIMER J, MCNAMEE C, NORRIS A, SANSEAU P, CAVALLA D, PIRMOHAMED M. 2019. Drug repurposing: Progress, challenges and recommendations. Nature Reviews Drug Discovery 18: 41–58.
ROBERTS CM, MCCLEAN CJ, VERON JEN, HAWKINS JP, ALLEN GR, MCALLISTER GE, MITTERMEIER CG, SCHUELER FW, SPALDING M, WELLS F, VYNNE C, WERNER TB. 2002. Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295: 1280–1284.
SANTOS R, URSU O, GAULTON A, BENTO PA, DONADI RS, BOLOGA CG, KARLSSON A, AL-LAZIKANI B, HERSEY A, OPREA TI, OVERINGTON JP. 2017. A comprehensive map of molecular drug targets. Nature Reviews Drug Discovery 16: 19–34.
SCHWARTZ GG, OLSSON AG, ABT M, BALLANTYNE CM, BARTER PJ, BRUMM J, CHAITMAN BR, HOLME IM, KALLEND D, LEITER LA, LEITERSDORF E, MCMURRAY JGV, MUNDL H, NICHOLLS SJ, SHAH PK, TARDIF JC, WRIGHT RS. 2012. Effects of Dalcetrapib in Patients with a Recent Acute Coronary Syndrome. New England Journal of Medicine 367: 2089–2099.
SPARANO JA, GRAY RJ, MAKOWER DF, PRITCHARD KI, ALBAIN KS, HAYES DF, GEYER CE JR, DEES EC, PEREZ EA, OLSON JA JR, ZUJEWSKI JA, LIVELY T, BADVE SS, SAPHNER TJ, WAGNER LI, WHELAN TJ, ELLIS M, PAIK S, WOOD WC, RAVDIN P, KEANE MM, GOMEZ MORENO HL, REDDY PS, GOGGINS TF, MAYER IA, BRUFSKY AM, TOPPMEYER DL, KAKLAMANI VG, ATKINS JN, BERENBERG JL, SLEDGE GW. 2015. Prospective Validation of a 21-Gene Expression Assay in Breast Cancer. New England Journal of Medicine 373: 2006–2014.
TARDIF JC, RHEAUME E, PERREAULT LPL, GREGOIRE JC, ZADA YF, ASSELIN G, PROVOST S, BARHDADI A, RHAINDS D, LLALLIER PL, IBRAHIM R, UPMANYU R, NIESOR EJ, BENGHOZI R, SUCHANKOVA G, LAGHRISSI-THODE F, GUERTIN MC, OLSSON AG, MONGRAIN I, SCHWARTZ GG, DUBE MP. 2015. Pharmacogenomic Determinants of the Cardiovascular Effects of Dalcetrapib. Circulation: Cardiovascular Genetics 8: 372–382.
[UNDP] United Nations Development Program. 2017. Press Release: Philippines to set voluntary commitments to protect the oceans. Retrieved from http://www.ph.undp.org/content/philippines/en/home/presscenter/pressreleases/2017/05/16/philippines-to-set-voluntary-commitments-to-protect-the-oceans.html
WESTFALL JM, MOLD J, FAGNAN L. 2007. Practice-Based Research—“Blue Highways” on the NIH Roadmap. Journal of the American Medical Association 297: 403–406.
WHITE AT, VOGT HP, ARIN T. 2000. Philippine coral reefs under threat: The economic losses caused by reef destruction Marine Pollution Bulletin 40: 598–605.