15
FinnGen ecosystem projects: PreMed Jaakko Lähteenmäki 4.12.2019, Biomedicum, Helsinki www.vtt.fi/premed
FinnGen ecosystem projects:PreMed
Jaakko Lähteenmäki
4.12.2019, Biomedicum, Helsinki
www.vtt.fi/premed
Data-driven precision medicine opportunity
2
Data exploitation
National registers
Patient recordsSocial servicescustomer data
Personal health services
Research registers
Population surveys
Biobankresources
Pharma & diagnostics
Food and nutrition
Healthcare
Personal devices & apps
VTT – beyond the obvious4.12.2019
PreMed – data-driven precision medicine ecosystem Time span: May 2017 - December 2020
Budget: 1166 k€
Funding: Business Finland, VTT, Companies
Overall objective:
• promote the development of a data-driven precision medicine ecosystem in Finland
Detailed objectives:
• collect and disseminate information of on-going national and international activities
• assess precision medicine ecosystem needs and bottlenecks
• identify new business strategies and models
• provide recommendations to public bodies
• carry out a biobank study to assess the relevance of exploiting pharmacogenomics
in a clinical use case
3
Exploitdata fromFinnGenproject!
• interviews• system
simulation
http://www.vtt.fi/premedVTT – beyond the obvious4.12.2019
Health & socialservicessoftware
Healthcaresystem
Data controller
Pharmaceutical company
Food and nutrition company
Data management and analytics provider
CitizenPersonalized food products
EHR&PHR solutions
New medicines forright patients
Point-of-care testingsolutions
ICT company
Remote monitoringsolutions
Data management and analytics services
Research & analyticsresults
Data
Data Research services
Diagnosticscompany
Partners and ecosystem rolesin PreMed project
Healthcare services
Research &analyticsresults
Fazer
4.12.2019
Active tasks and contributors in 2019-2020
5
Task 9: Management
Task 8: Networking & Dissemination
Task 7: Biobank study - research
Task 6: Biobank study – organisation
Task 3: System analysisPeter Ylén
Tomi Sorasalmi
Anna-Leena Vuorinen
Juha Pajula
Jaakko Lähteenmäki
Jari Ahola
Mark van Gils
Richard Fagerström
VTT – beyond the obvious4.12.2019
External advisors
Kari Harno, UEF
Mika Lehto, HUS
Mikko Niemi, UoH and HUS
Tanja Nieminen, Medaffcon Oy
PreMed – biobank study use case: pharmacogenomics
VTT – beyond the obvious6
EHR + genotype data
Decision on best drug and drug dose for the patient using all availabledata (incl. genotype)
4.12.2019
Pharmacogenomics example:
CYP2C9 gene variant association with warfarin
7
CYP2C9gene
chromosome #10 CYP2C9*1
wild type(normal)
CYP2C9*2
or
CYP2C9*3
allele
~35% of
Finnish
population
• Slower metabolism of warfarin• Increased
anticoagulation effect• Increased risk of
bleeding with normal warfarin dose
Research questions
• How much the risk for bleeding is increased in the Finnish population?
• Is it clinically and economically relevant to do a genome test to adjust the medication dose?
VTT – beyond the obvious4.12.2019
PreMed PGx study:Pharmacogenomics of antithrombotic drugs
Overall goal: investigate the feasibility of using genome data in the context
of antithrombotic therapy
• Gain evidence on the association between gene variants and
anticoagulation control of warfarin therapy.
• Assess the clinical and economic impact of using genotype data in
guiding warfarin therapy.
• Explore potential genotype-phenotype associations in the context of
antithrombotic therapy in general
• To assess the current usage of pharmacogenetic information in the
context of antithrombotic therapy.
8VTT – beyond the obvious4.12.2019
Needed data resources for the PreMed PGx study
Genome data from biobanks
EHR data from hospital data lakes (via biobanks)
Laboratory data
THL register data (Hilmo&Avohilmo)
Kela register data (drug purchases)
9VTT – beyond the obvious4.12.2019
Application
1 /2019
2 /2019
3 /2019
4 /2019
5 /2019
6 /2019
7 /2019
8 /2019
9 /2019
10 /2019
11 /2019
Ethicalboard
HelsinkiBiobank
Auria Biobank
THLBiobank
THLRegistry
Kela
Progress of data collection
10
planned
realized
continuing application submission
positive decision
MTA ready
adjustment requested
MTA signed
Data delivery
waiting THL registry permit
waiting THL registry permit
waiting THL registry permit
Ecosystem simulation approach
11
Companies exploiting data or derived results:- pharma- diagnostics- food- medical devices - ICT- EHR/PHR
software
data/samples
Data and biosample resources:- biobanks- health and
social care registers
Centralized access services:FindataFINBB
Centers of excellence
Public investments
Research services
Academic research
Support services (omics, data management and analytics, software)
data/samples
fees&enrichment
fees&enrichment
results
fees
knowledge
feesservicesfeesservicesfeesservices
Healthcare system
Citizen
products/services
Societal/economic benefits
Data-driven precision medicine ecosystem
Model implementaion in Vensim™ tool
Biobank Service feesfrom commercial
projects
Publicinvestments in
biobanks
Publicinvestments
in serviceoperator
Service operatorservice fees
+
Available dataresources for
secondary use
Data andsamples inBiobanks
Serviceoperator
(FINDATA)progress
Service operatordevelopment
R&D projects
+
Delay in research proposalevaluation and data acquisition
(data permit application)
R&D projectsending succesfully
R&D projects endingwithout new products
R&D projectswaiting to
startR&D projects
startsR&D projectproposals
Companies'Ability to
Exploit Data
Availability andcompetence of
support services
Increase insupport services
Biobank and serviceoperator unit price per
data
+
effect of delay onwillingness of R&D
start
Perceived benefitsof R&D projects
R
biosamples anddata to biobank
Total investments inbiobank consents
projectsuccess ratio
+
r&d projectduration
-
Effect of R&D coston project start
+
efficiency serviceoperator
development
ref cost
ref delay
Registerdata
register datageneration
Data generation inhealth and social service
processes
ref successratio
efficiency of publicinvestment on support
services
+
init registerdata
Ref bio data
init serviceoperator progress
init data andsamples in biobanks
effect serviceoperator on
delay
minimumdelay
<TIMESTEP>
max serviceoperator
developmentrate
Enrichingdata
Data andanalyticsusers in
academicresearch
Newacademicresearch
users
Research projectproposals
New academicresearch project
proposals
<Delay in research proposalevaluation and data acquisition
(data permit application)>
Effect ofavailable dataresources onacademic use
Init potential number ofresearch project starts
per year
Publications
newpublications
academicresearchending
Availability ofMyData
-
Effect of apublication oncompetence
center
publications perresearch project
Enriching perproject
effect of projectsuccess ratio on R&D
starts
Strength of R&Dcosts on project
starts
+
Data and analyticsR&D (RWE project
volume)
MEuro perproject
service operatorunit price per data
+
delaystrength
R
Init number ofproposals
Public investments insupport services
research
Public investments inNational Genome
Centre
Public investments incompetence center
Competence centerSupport for further
development ofresearch ideasDevelopment of
Competence center'ssupport ability
Availability ofGenome Centre
Services andData
Public investments insupport services BioIT
Support ServiceAvailability Ratio
+
Ref SupportService
AvailabilityRatio
+
Strenght ofSSAR onCAtED
Increase in GenomeCentre Services and
Data
Init availability ofgenome centre
Avg duration ofacademic rereach
project
Strenghtof CAtEDon PSR
SSARon/offswitch
+
Degradation ofcompetence center's
support ability
Labor intensity ofapplying data
Data integration capabilityALKUARVOKSI VAIKKA
50%
Effect of newpublications on R&D
ideas
Ref number ofpublications in a
year
Strength ofEoNPoRDI
Effect of investmentson Genome Centre
Init laborintensity
Strength of SOPon LIoBD
Effect of laborintensity onR&D project
ideas
Ref laborintensity
Strenght ofintegration
of data
Effect of CAtEDon PSR+
+
<ref successratio>
Project successratio on/off switch
Effect of publicinvestment oncompetence
centers
Strength of publicinvestment on
CCSffDoRI
Degradation timeof CCSA
Delay forcompetencedevelopment
Support servicedevelopment
+
Effect ofCCSfFDoRI onproject ideas
Sthrenght ofCCSfFDoRI
Delay for GenomeCentre servicedevelopment
Effect of GenomeCentre Availability on
NARPP
Strength ofEoGCA
Public investmentduration Biobanks
Public investmentstart time biobanks
Research projectplanning delay
Effect ofCCSfFDoRI onresearch ideas
R&D projectplanning delay
Obsolescence ofcompetencies
Strength ofCCSfFDoRI onresearch ideas
+
Degradationtime
-
Supportservice
availabilitygap
-
-
+
Adjustment time ofsupport servicedevelopment
publications perR&D project
Expectedobsolescence ofcompetencies+
+
-
R&D projectgrowth ratio
Init Researchproject proposals
Init Data and analyticsusers in academic
research
Research projectgrowth ratio
Init number ofR&D projects
Public investmentduration Supportservices research
Public investmentduration Support
services BioIT
Public investment starttime Support services
research
Public investment starttime Support services
BioIT
Public investments insupport servicesresearch policy
Public investments insupport services BioIT
policy
Public investments inbiobanks recruitments
policy
Public investmentduration competence
center
Public investmentduration service
operator
Public investment starttime service operator
Public investment starttime competence
center
Public investment starttime Genome Centre
Public investmentduration Genome
Centre
Public investments inNational Genome
Centre Policy
Public investments inservice operator Policy
Public investments incompetence center
Policy
Total biobankservice fees
+
Annual R&Dexpenditures
+
Annual R&Dexpenditures per
project
+
Biobankconsents
Potentialpersons inbiobank
Signign biobankconsent
Populationsize
Populationmultiplier
+
Resources toconsents
+
Public investments inAcademic Research
Public investment starttime Academic
Research
Public investmentduration Academic
Reserach
Public investments inAcademic Research
Policy
Biobank service feesfrom academic projects
+
Biobank servicefees for academia
+
+
Units of data perperson
Average number ofpersons in a biobank
project
Average number ofenriched data per person
per project
++
Dataaccumulation
Data accumulationunits of data perperson per year
Public investment inbiobank resources
Cancelingbiobank consent
External biobankconsent cancellation
Required resourcesneeded to get onesignature EURO
+
Ref requiredresources need for a
signature
+
+
R&D projectsending
++
Averagenumber ofdata perperson
Data removal
++
Init biobankconcents
Biobankconsent ratio
SOD start time
<Time>
Biobankconsent
collectioncapabilityConsent collection
capabilitydevelopment+
-
Learning bydoing divider
Init biobank consentcollection capability
HISTORY Publicinvestment in
biobanks
Required resourcesneeded to get onesignature MEURO
+
-
+
+
Potential number ofR&D data project starts
Share of potentialto data projects
Lookup shareof data
Effect of available dataon share of data
projects
Max amount ofdata
<Units of dataper person>
<Populationsize> Data
multiplier
Init data integrationcapability
Academicpublishing delay
Average expenditureof research project
Funding available fornumber of projects
Total number of potentialresearch project starts
per year
<Avg duration ofacademic rereach
project>
External biobankconsent cancellation
start time
External biobankconsent cancellation
duration
External biobankconsent cancellation
ratio
Funding availablefor starting projects
Euro toMEuro
VTT – beyond the obvious4.12.2019
Example of initial simulation results with limited model functionality
13
5
15
25
35
45
55
65
75
85
0 1 2 3 4 5
Vo
lum
e o
f R
WE
pro
ject
s (M
€)
Years
Investments in biobanks and service operator (5M€ + 5M€ per year)
Investments in biobanks (5M€ per year)
Investments in service operator (5M€ per year)
Baseline (no investments)
VTT – beyond the obvious4.12.2019
Conclusions and observations
Support of joint biobank projects needed
• joint services
• harmonization of processes and practices
• project organization and leadership
Improvement of registry data access needed
• high expectations towards Findata – attention needed for:
• sufficiency of resources
• relation with biobanking
• data anonymization process
Support for impact analysis needed
• ecosystem simulation model being developed
14VTT – beyond the obvious4.12.2019
