1. capabilities of PHILIPPINE GENOME CENTER facilities
( pgc-dscf | pcari-sgcl | pgc-cfb )
MA. ANITA M. BAUTISTA, PhD
Director
DNA Sequencing Core Facility
12 Nov 2016

2. CORE FACILITIES Facility Name: DNA Sequencing Core Facility (DSCF)
Shared Genomics Core Laboratory (SGCL)
Core Facility for Bioinformatics (CFB)
Name of Implementing Institution:
Philippine Genome Center (PGC)
Philippine-California Advanced Research Institutes (PCARI)
Funding Agency:
Commission on Higher Education (CHED)

3. PGC-DSCF: overview
provides high quality and ultramodern sequencing and analytical services to the Philippine scientific community
embarks on cross-disciplinary research programs geared towards the discovery and functional analyses of genes of biological, forensic, biomedical, and agricultural importance for the development of innovative diagnostic and therapeutic strategies and technologies
aims to create a hub for the education and training of researchers and scientists to fill the talent gap in genomics

4. SCIENCE RESEARCH SPECIALIST I LABORATORY TECHNICIAN
pgc-dscf team
Ma. Anita Bautista, Ph.D.
DIRECTOR
Juan Miguel Recto, M.Sc.
SCIENCE RESEARCH SPECIALIST I
Kevin Cruzado
Shiela Araiza
LABORATORY TECHNICIAN
Kris Punayan

5. RESOURCES:
DSCF currently owns a high-throughput capillary DNA sequencer and three Next Generation Sequencing (NGS) platforms.
Ion Proton
10Gb
200bp
Illumina MiSeq
7Gb
2x150bp
Ion Torrent PGM
100Mb-1Gb
400bp
3730xl DNA Analyzer
96-Capillary
800bp read length

6. RESOURCES:
DSCF is also equipped with other sophisticated machines for nucleic acid extraction and analysis.
MultiNA Microchip Electrophoresis System
Applied Biosystems 7500 Fast Real-Time PCR
Varioskan Multimode Microplate Reader
KingFisher Flex Magnetic Particle Processor

7. RESOURCES:
Other sophisticated machines for use in standard molecular biology and NGS work
QIAgility Liquid Handler
Pippin Prep
Covaris M220 Focused Ultrasonicator
Qubit Fluorometer

8. SERVICES: Next generation sequencing
WHOLE GENOME SEQUENCING
RNA SEQUENCING
TARGETED SEQUENCING
METAGENOMIC SEQUENCING

9. SERVICES: CAPILLARY SEQUENCING and OTHER SERVICES
CAPILLARY DNA SEQUENCING AND FRAGMENT ANALYSIS
NUCLEIC ACID EXTRACTION, QUALITY ASSESSMENT AND QUANTIFICATION

10. CLIENT PROFILE AND INCOME
53% of the clients are UP-based
Bulk of the income (70%) come from NGS

11. CLIENT PROFILE AND INCOME
- An average of 16 New Clients per quarter since launch

12. pcari-sgcl: overview
purpose-built resource which seeks to expand significant collaborations, networking, and information exchanges within the Philippine scientific community from various institutions
will give additional support to the Philippine Genome Center network
seeks to strengthen national laboratory capacity for high throughput genomics and sequence-to-function research

13. Eva Maria Cutiongco-de la Paz, M.D.
pcari-sgcl team
Eva Maria Cutiongco-de la Paz, M.D.
PROJECT LEADER
Cynthia Saloma, Ph.D.
CO-PROJECT LEADER
Zenaida Magbanua, Ph.D.
PDO V (LAB MANAGER)
Beverly Ann Boyboy
RESEARCH ASSISTANT
Sarah Mae Penir
RESEARCH ASSISTANT
Shiny Cathlynne Yu, M.Sc.
RESEARCH ASSISTANT
Eileen Montes
PDO I

14. Pacific Biosystems Sequel
NEW GENOMICS TECHNOLOGIES USING STATE-OF-THE ART NEXT GENERATION SEQUENCERS
Pacific Biosystems Sequel
Illumina HiSeq 3000
(Max Output: 750 Gb)
Illumina NextSeq 500
(Max Output: 120 Gb)
Illumina MiSeq FGx
(Max Output: 15 Gb)
Illumina MiSeq

15. other next generation sequencing-related equipment
Agilent TapeStation 2200
Sage Science Pippin Prep
Applied Biosystems ABI 7500
Real-time PCR
Covaris M220
Qubit 3.0

16. microscopes Leica LMD6 Laser Microdissection Microscope
Carl Zeiss Axio Imager M2
Fluorescence Microscope

17. KingFisher Flex System Affymetrix GeneTitan Microarray
Other equipment
Varioskan Lux
Microplate Reader
KingFisher Flex System
Affymetrix GeneTitan Microarray

18. PGC-CFB Team Baltazar Aguda, Ph.D. PGC EXECUTIVE DIRECTOR /
CFB OFFICER IN CHARGE
Francis Tablizo, M.Sc.
INFORMATION AND OPERATIONS
OFFICER
Marylette Roa, M.Sc.
SENIOR BIOINFORMATICS
SPECIALISTS
El King Morado
SENIOR BIOINFORMATICS
SPECIALISTS
Joshua Gregor Dizon
DATABASE AND NETWORK
ADMINISTRATOR

19. PGC-CFB: Overview One of the three core facilities, established to:
enable researchers to efficiently process, manage, curate, share and archive massive amounts of genomic and related data
facilitate the development of local expertise in Bioinformatics
pursue research programs relevant to PGC’s thrusts

20. RESOURCES: Computers and Servers
The CFB currently owns three Large-memory servers: a BlueGene/P supercomputer, two storage servers and a xeon-phi server. Installed in these servers are ~150 open-source bioinformatics tools and databases.
BlueGene/P
Large-memory Servers
Xeon Phi
Storage Servers

21. PGC-CFB hosts bioinformatics trainings and workshops.
SERVICES
Direct Access clients are given remote access to the PGC-CFB’s servers.
Custom Service
PGC-CFB’s staff implements bioinformatics workflows in behalf of the client.
Bioinformatics
Trainings
PGC-CFB hosts bioinformatics trainings and workshops.

22. FUTURISTIC GOAL:
“to transform from a sequencing center to a genomic science analysis resource”
need to develop and apply new advanced and high- throughput technologies, approaches and computational resources
need to collaborate with the best scientists in relevant research areas
need for increased number of regular staff and long-term funding

23. Thank you for listening.