genomics r&d roadmap (2012-2018)pcieerd.dost.gov.ph/images/pdf/2017/roadmaps/genomics.pdf ·...

GENOMICS R&D

ROADMAP (2012-2018)

Philippine Council for Industry, Energy and

Emerging Technology Research and Development

Outline

PCIEERD-DOST

Genomics R&D Roadmap and S&T Activities

Health

Agriculture/ Fisheries/ Livestock

Biodiversity

Other Applications

Nutrigenomics

Forensics

Ethnicity

Core Facilities

Genomics as a technological platform to

revolutionize R&D in health, agriculture and

biodiversity for socio-economic development

S&T Investments &Activities

Outputs

GENOMICS R&D ROADMAP (2012-2018)2012

2013

2014

2015

2018

2017

PCIEERD-DOST

Health

PCIEERD-DOST

Diagnostics for infectious diseases

Diagnostics for non-communicable diseases

Vaccine development

Biosurveillance programs for epidemics

Gene library / Bio bank

Health

Application of

Genomics


Outputs

GENOMICS R&D ROADMAP (2012-2018)

Diagnostics

for dengue

2012

Bio-

surveillance

systems for

epidemics

Diagnostics

for TB,

A1N1,

Cancer

2013

Diagnostics

for Malaria,

CVD,

Hematologic

Disorder

Stem cell

bank2014

For the promotion of Filipino health (Filipinized personal

medicine) and the prevention and management of public

health problems

PCIEERD-DOST

Diagnostics

paragoni-

miasis

Vector

resistance

markers

Diagnostics

asthma /

allergies,

autism2017

Anti-cancer drug

resistance

markers

Diagnostics

filiiarisis

2018

Diagnostics for

neglected

tropical diseases (leshmaniasis,H. pylori &

hypochlorydria)

Dengue

recombinant

protein vaccine

Antibody gene

library

Diagnostics

respiratory

panels (e.g.

pneumonia)

2015

2016

Diagnostics,

H. Pylori, &

hypochlor-

hydria

Diagnostics

Schistoso-

miasis,

S & T Activities - HEALTH

2012

Clinical utility and field-testing of dengue kits

Commercialization and utilization of dengue kits

2013

Genome variation detection for TB, A(H1N1) and cancer

Development of genome-based kits for TB, A(H1N1) and cancer

Collection of data for biosurveillance

Operational Biosurveillance systems for epidemics

PCIEERD-DOST


2014

Genome variation detection for Malaria

Development of genome-based kit for Malaria

Clinical utility and field-testing for CVD kit

Commercialization and utilization of CVD kit

Genome variation detection for Hematological Disorder

Development of stem cell bank

PCIEERD-DOST


2015

Genome variation detection for neglected tropical diseases (leshmaniasis), H.

pylori, and hypochlorhydria

Development of genome-based kits for neglected tropical diseases

(leshmaniasis), H. pylori, and hypochlorhydria

Genome variation detection for Respiratory panels: acute pneumonia, chronic

pneumonia, opportunistic respiratory infection

Development of genome-based kits for Respiratory panels

Genome variation detection for Schizophrenia, Bipolar Disorders and

Diabetes

Development of genome-based kits for Schizophrenia, Bipolar Disorders and

Diabetes

Development of dengue recombinant protein vaccine

Collection of Philippine Antibody Gene Library PCIEERD-DOST


2016

Diagnostics for neglected tropical diseases (schistosomiasis)

2017

Diagnostics for neglected tropical diseases (paragonimiasis)

2018

Diagnostics for neglected tropical diseases (filiiarisis)

Anti-cancer drug resistance markers

Agriculture/Fisheries/

Livestock

PCIEERD-DOST

Endemic Crops & Staples

Microbes

Fisheries / Aquaculture

Livestock

Agriculture /

Fisheries /

Livestock


Outputs


Marker-assisted breeding for varietal improvement

of economically important endemic crops & staples

2017

GM Mango

with Delayed

ripening

cDNA

Library of

rice

PCIEERD-DOST

Hybridity &

sex markers

of papaya

ABTV

resistant

abaca

2012

Mol.

markers for

virus

resistance in

rice

DNA

fingerprint

staples

DNA

fingerprint of

mango

Hybridity &

sex markers

of abaca &

pili

2013

Mol. marker

of rice inbred

line w/

bacterial

blight

resistance,

submergence

tolerance

Mol. Marker

Ht rice 2014

Mol. markers

for ABTV

resistance

Fingerprint of

Phil.

bananas

Rice

Genomics

Database

PCR

detection kit

anthracnose

Mol. marker

for blast

resistance in

rice

ABTV

resistant

2015

Delayed

ripening in

‘saba’

Gene

discovery

for high oil

quality/yield

in coconut

Mol. marker

downy

mildew

resistance in

corn

2016

QTL for

drought

resistance in

eggplant

Mol. marker

for corn borer

Mol. marker

rice w/ tungro

virus

resistance &

Herbicide

tolerance

2018

Drought

resistant

eggplant

variety

Bt rice

GM sweet

potato (coat

protein)

S & T Activities - AGRICULTURE

Endemic Crops and Staples

2012

Characterization and development of molecular markers of papaya

varieties, validation of hybridity and sex determination at early stages

Characterization and development of molecular markers for abaca

bunchy top virus (ABTV) resistance and good fiber quality for use in

marker assisted breeding

Marker-assisted development for tungro virus resistance in rice

DNA fingerprinting of loci for selected economically important traits

2013

Characterization and development of molecular markers of abaca

varieties and validation of hybridity

Characterization and development of molecular markers of pili varieties

and sex determination at early stages

PCIEERD-DOST


2013…cont’d. Endemic Crops and Staples

DNA fingerprinting of mango

Marker-assisted development of rice inbred line w/ bacterial blight resistance,

submergence and herbicide tolerance

2014

Marker-assisted breeding for ABTV resistance and good fiber quality in abaca

Characterization and development of molecular markers of the Philippine

bananas

PCR based detection kit for anthracnose

2015

Marker assisted development for ‘bugtok’ disease resistance and delayed

ripening in ‘saba’ banana

Gene discovery for high oil quality and yield in coconut

Marker assisted development for downy mildew resistance in cornPCIEERD-DOST



2016

Identification and characterization of potential economically important

antimicrobials and enzymes through metagenomic approaches

Identification and mapping of quantitative trait loci (QTL) for drought

resistance in eggplant

Marker-assisted development of rice inbred line w/ tungro virus resistance,

herbicide tolerance, and corn borer resistance

2017

Development of GM Mango w/ delayed ripening

Marker assisted breeding for corn stalk rot complex, bunchy top virus

resistance in banana

cDNA library of rice under stressed and unstressed environmental

conditionsPCIEERD-DOST



2018

Marker assisted breeding for low phytic acid in rice

Marker assisted breeding for crack resistance in rice

Marker assisted breeding for yield in rice

Development of Bt rice

DNA fingerprint of Feathery Mottle Virus (FMV) in sweet potato

Development of GM Sweet Potato with SPFMV-R (coat protein)

Development of Banana Linkage Map

Marker-assisted development for Fusarium wilt resistance in banana

PCIEERD-DOST

Agriculture/

Fisheries/

Livestock


Outputs


2018

DNA fingerprinting of biofertilizer, biopesticides, &

probiotics for improvement of industrial products

2017

Full

characteriz’n

Mycogroe,

Mykovam &

Microbial

Rennet

PCIEERD-DOST

Improved

biofertilizers,

biopesticides

& probiotics

2012

Improved

screening of

microbial

culture

collection

DNA finger-

print of

biofertilizers,

biopesticides

& probiotics

2013

DNA

fingerprint of

enzymes-

microbial

rennet 2014

DNA finger-

print of

biopesticides

(virus, fungi),

industrial

enzymes

(yeast)

Screening of

isolates for

selected

applications

2015

Thermo-

tolerant

(ethanol

products)

Mol. markers

for key

isolates –

microbial

culture

collection

DNA

fingerprint of

Azospirillum

sp. (BioN)

2016

Full

characteri-

zation of

active

ingredients

of BioN,


Microbes

2012

Development of improved biofertilizers, biopesticides, probiotics

Improve the screening of microbial culture collection

2013

DNA Fingerprinting of Biofertilizer – BioN, Azospirillum sp.

DNA Fingerprinting of Biopesticides – Bt and Bacteria

DNA Fingerprinting of Probiotics – Bacteria

DNA Fingerprinting of Enzymes – Microbial Rennet

DNA Fingerprinting of Bacteria and Fungi for Industrial Enzymes

DNA Fingerprinting of Microbial Culture Collection for Industrial Enzymes

(NSRI and PNCM)

PCIEERD-DOST


Microbes

2014

DNA Fingerprinting of Biopesticides – Virus, Fungi & Industrial Enzymes

(yeast); Screening of Isolates for selected applications

2015

Development of ethanol products from thermotolerant microbes

Marker-assisted development for key isolates – microbial culture

collection

DNA Fingerprinting of Azospirillum sp. (BioN) as Biofertilizers

2016

Full Characterization of Active Ingredients of Commercial Products - BioN,

Azospirillum sp.

PCIEERD-DOST


Microbes

2017

Full Characterization of Active Ingredients of Commercial Products

Ectomycorhiza – Mycogroe

Full Characterization of Active Ingredients of Commercial Products

Endomycorhiza – Mykovam

Full Characterization of Active Ingredients of Commercial Products –

Microbial Rennet, Azospirillum sp.

Full Characterization of Active Ingredients of Commercial Products –

Yeast for Ethanol Production

2018 - none

PCIEERD-DOST

Agriculture/

Fisheries/

Livestock


Outputs



of economically important aquaculture resources

PCIEERD-DOST

Selection for

disease

resistance

developed

Assembled/

annotated

partial

genome

sequences

selected toxic

microalgae

Mol. markers

Heliopora,

Holuthuria,

Stichopus,

Tawilis,

Tilapia

2013

Mol. markers

for resistance

to white spot

syndrome

virus

Assembled/

annotated

genome

sequences

Kappaphycus

& agar

DNA

fingerprint of

milkfish

stocks

DNA

fingerprint of

abalone &

mudcrab

2012

Vaccine

DNA & RNA

High health

shrimp

spawners &

seedstock

Mol.

markers

milkfish

Toxin

biosynthesis

genes (HAB)

Selective

breeding

abalone &

mudcrab

Mol.

markers

Montipora

2014

HAB

detection

kits

Genetically

improved

abalone &

mudcrab

Germplasm

banks

(seaweeds)

Gene profile

of bleaching-

tolerant coral

symbiont

2015

Field-tested

abalone and

mudcrab

stocks

Mol.

markers

acid-tolerant

corals

Expression

profile of

Stichopus2016

Genotypic

profile of

resilient

coral

species

2018

Enhanced

reproductive

/ growth

traits

evaluated

High health

shrimp

spawners &

seedstock 2017

Agriculture/

Fisheries/

Livestock


Outputs



of economically important livestock resources

PCIEERD-DOST2012

DNA-based

diagnostic

kit for rapid

screening of

bull semen

for FMD

virus

2014

2015

2016

2018

2017

Mol. markers

buffalo

breeds &

cross breeds

for high

carcass yield

and draft

power

2013

Mol. markers

dairy buffalo

breeds w/

high milk

yield & quality

Viable cloned

buffalo

embryo


Livestock

2013

Marker-assisted development for buffalo breeds and cross breeds for

high carcass yield and draft power

Marker-assisted development for dairy buffalo breeds with high milk yield

and quality

Production of viable transferable cloned embryo

2014

Development of DNA-based diagnostic kit for rapid screening of bull

semen for Foot and Mouth Disease (FMD) virus

PCIEERD-DOST

Biodiversity Application

of Genomics


Outputs


Genes from

marine &

microbial

organisms

encoding

neuroactive,

antimicrobial

anticancer

Genes from

micro-

organisms

encoding

bioenergy &

industrial,

environ-

mental, food

& research

enzymes

2012

Genes from

plants

encoding

medicinal,

nutraceutical

compounds

Compounds

for pain,

aging,

infections,

cancer, and

other

diseases

2013

Priority

compounds

for pain,

aging,

infections,

cancer, and

other

diseases

Standardized

extracts for

medicinals &

nutraceuticals

2014

Small-scale

enzyme

bioreactors

Plantlets of

best genetic

varieties of

medicinal

and nutra-

ceuticals

2015

Conservation and harnessing Philippine biodiversity for

sustainable drug discovery and bioenergy production

2016

Lab-tested

drug

candidates

Completed

survey of

selected

genome-

based

Philippine

biodiversity

2017

Plantings of

best genetic

medicinal plant

varieties

2018

Databank

of genetic

varieties

PCIEERD-DOST

S & T Activities - BIODIVERSITY

2012

Gene sequencing design, run & data analysis, & identification of key

genes of marine & microbial samples for drug discovery, bioenergy &

industry

Sample collection & functional characterization of endemic varieties of

plants, animals & mcoroorganisms for medicinals, nutraceuticals, food,

industry, ecotourism & conservation

2013

Isolation, chemical, biochemical & functional characterization of genes,

small molecules & enzymes for drug discovery, bioenergy & industry

Gene sequencing design, run & data analysis, identification of key genes

of plants, animals & microorganisms for medicinals, nutraceuticals, food,

industry, ecotourism & conservation

PCIEERD-DOST


2014

Structure determination, bioactivity testing & SAR (structure activity

relationship) studies of bioactive compounds

Genetic engineering of microorganisms to express enzymes that produce

ethanol & lactic acid

Isolation, identification & functional characterization of compounds,

enzymes & best genetic varieties

2015

Chemical modification, synthesis & SAR (structure activity relationship)

studies of bioactive compounds

Small-scale genetically engineered microbial production of ethanol & lactic

acid

Isolation, identification & functional characterization of compounds,

enzymes & best genetic flora & fauna varieties

PCIEERD-DOST


2015..Cont’d.

Gene-marker assisted selection of best varieties for optimal growth of

plants & production of medicinal compounds

Genetic engineering of microorganisms to express thermophile enzymes

Field-based correlation of gene-markers and best properties of

endangered, ecotourism & food species/varieties

2016

Chemical modification, synthesis & SAR (structure activity relationship)

studies of bioactive compounds

Establishment of small-scale genetically engineered microbial production

of drug candidates

Energy biomass & substrate optimization for ethanol & lactic acid

production

Gene-marker assisted selection of best varieties for optimal growth of

plants & production of medicinal compoundsPCIEERD-DOST


2016…Cont’d.

Setting up of farm plots for planting best gene-marker selected best

varieties of medicinal plants

Small-scale genetically engineered microbial production of thermophilic

enzymes

Gene-marker assisted selection, small-scale culture & breeding of best

natural varieties adapted to natural habitat

2017

Molecular target & animal testing of drug candidates

Optimization of small-scale genetically engineered microbial production of

drug candidates

Pilot-scale genetically engineered microbial production of ethanol & lactic

acid

Isolation & bioactivity testing of medicinal compounds

PCIEERD-DOST


2017… Cont’d.

Preparation & clinical trials of standardized nutraceutical herbal extracts

Optimization of thermophilic enzymes with industrial substrates & processes

Pilot-scale culture & breeding of best natural varieties adapted to natural

habitat

2018

Clinical trials of drug candidates

Small industry-scale genetically engineered microbial production of ethanol &

lactic acid

Clinical trials of medicinal compounds and standardized nutraceutical herbal

extracts

Pilot-scale genetically engineered microbial enzyme production for industrial

processes

Small industry-scale culture & breeding of best natural varieties adapted to

natural habitat for commerce & restocking in the wild

PCIEERD-DOST

Other Applications

of Genomics

PCIEERD-DOST

Nutrigenomics Forensics Ethnicity Core Facilities

Gene database, designer foods and personalized

nutrition for the prevention

& management of public

health problems

Nutrigenomics


Outputs


2016

designer

foods &

nutrition

protocol for

osteoporosis

2012

Genetic

database on

Nutritional

Diseases2013

Genetic

database on

Nutritional

Diseases

PCIEERD-DOST

2017

Functional

foods and

personalized

nutrition for

asthma and

allergies&

obesity

2018

Functional

food/designer

foods for iron

deficiency

anemiaGenetic

database on

Undernutrition

2014

Functional

food/designer

foods for

cancer and

diabetes

Personalized

nutrition

protocol for

cancer and

diabetes

2015

Functional

food/

designer

foods for

CVD

Personalized

nutrition

protocol for

CVD

S & T Activities - Nutrigenomics

2012

Development of genetic database on Nutritional Diseases

(SNPs for 5 major lifestyle,diet-related diseases) among

Filipinos

2013

Development of genetic database on Nutritional Diseases

(SNPs with Cancer and Diabetes) among Filipinos

2014

Development of Genetic database on Undernutrition (e.g.

Iron and Iodine Deficiency)

Development of Functional food/designer foods and

personalized nutrition protocol for cancer and diabetes

PCIEERD-DOST

S & T Activities - Nutrigenomics

2015

Development of functional food/designer foods and personalized

nutrition protocol for CVD

2016

Development of functional food/designer foods & personalized

nutrition protocol for osteoporosis

2017

Development of functional foods and personalized nutrition for

asthma and allergies

Personalized nutrition protocol for obesity

2018

Functional food/designer foods and personalized nutrition for

undernutrition and Iodine Deficiency

PCIEERD-DOST

Integration of Genomics in the Medico-Legal SystemFORENSICS


Outputs


Biosecurity

system for

forensics

2015

2016

International

Laboratory

Accreditation

as a Forensic

DNA

Laboratory

2012

Sexual

assault

investigation

kits (SAIK) 2013

Forensic

courses/

workshops

PCIEERD-DOST

Filipino

Identity

2014

Collection kits

for different

types of

forensic

samples

Forensic

Science

integrated in

academic

subjects

2017

Forensic

accreditation

programs

2018

National

criminal

DNA

database

S & T Activities - Forensics

2012

Development of Sexual assault investigation kits (SAIK)

2013

Conduct of forensic courses/workshops

2014

Development of collection kits for different types of forensic samples

Integration of Forensic Science in academic subjects

2015

Development of Biosecurity system for forensics

2016

International Laboratory Accreditation as a Forensic DNA Laboratory

2017

Establishment of forensic accreditation programs

2018

Development and maintenance of national criminal DNA database PCIEERD-DOST

Genomic study of Filipino ethnicity, which will yield

valuable information about our people’s genetic

history

ETHNICITY


Outputs


2014

2017

2018

2015

2012

Rizal

Genealogy

(lineage)

PCIEERD-DOST

2013

Genetic

databases of

Philippine

museum

samples

Filipino

population

genetic

database /

resource of

ethnolinguis-

tic groups

and regional

groups

2016

Repository of

Philippine

ethnic

information

Filipino

population

genetic

database /

resource

S & T Activities - Ethnicity

2012

Development of Rizal Genealogy (lineage)

2013

Development of databases of Philippine museum samples

2016

Establishment of repository of Philippine ethnic information

Development of Filipino population genetic databases / resource

PCIEERD-DOST

Supporting the National Genomics R&D AgendaDNA Sequencing &

Bioinformatics Core

Facilities


Outputs


High-

throughput

DNA

sequencing,

genotyping

and gene

banking

services

New

algorithms,

software,

tools for

fundamental

and applied

genomics

2014

Competent

human

resources

Technology

spinoffs from

genomic

information

2015

2016

Expanded

genomics

sequencing

services

integration of

nanotech

and

genomics in

prod’n of

nanodevices2017

Genomics

tranings/

workshops 2018

Genomics

technology

spinoffs

Operational

DNA

Sequencing

Core Facility

2012

Operational

high-

performance

computing

facility

Phase 1-

Manpower

development

and training

in genomics

and bioinfor-

matics

Enhanced

high-

performance

computing

facility

Medium

throughput

DNA

sequencing

and

genotyping

services

2013

Bioinfor-

matics

expertise

services

available

PCIEERD-DOST

S & T Activities - DNA Sequencing Core Facility

2012

Establishment of sequencing service infrastructure

Manpower development in genomics and bioinformatics

Setup Laboratory Information and Library System

Bacterial whole genome sequencing projects

2013

Capacity building for high-throughput NGS and bioinformatics

Setup linkages with international genome centers

Transcriptome of medicinal plant

Advocacy activities on genomics

2014

Campaign for personalized genomics, utilization of sequencing services in the

health sector

Participation in international genome sequencing consortium

Upgrade/expansion of sequencing services PCIEERD-DOST

S & T Activities - DNA Sequencing Core Facility

2015

Expansion of sequencing services

Advocacy activities, genomics technology promotion

2016

Expand manpower development and training of staff

Streamline activities and improve efficiency of operations

Expand client base

2017

Develop spinoff technologies from genomic information

Streamline sequencing services

2018

Upgrade/expansion of sequencing services

Advocacy activities, genomics technology promotion

PCIEERD-DOST

S & T Activities - Bioinformatics Core Facility

2012- 2015

Establishment of computing infrastructure and other resources

Implementation of bioinformatics manpower development programs

(trainings, workshops, conferences, etc.)

Implementation of research projects, including development of bioinformatics

/ computational biology algorithms, software, and software development tools

PCIEERD-DOSTPCIEERD-DOST

PCIEERD-DOST

Thank you

genomics r&d roadmap (2012-2018)pcieerd.dost.gov.ph/images/pdf/2017/roadmaps/genomics.pdf ·...

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