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Description of the current status and future needs of the Information Architecture and Data Management solutions for the national personalised medicine pilot project CONTRACTING AUTHORITY:MINISTRY OF SOCIAL AFFAIRS PROCUREMENT REFERENCE NUMBER: 160112 TARTU 2015 SULEV REISBERG HARRY-ANTON TALVIK KALEV KOPPEL SVEN LAUR JAAK VILO Software Technology and Applications Competence Centre (STACC) Quretec University of Tartu Information Architecture of Estonian Personalised Medicine Pilot Project ii Copyright © 2015 OÜ Tarkvara Tehnoloogia Arenduskeskus / Software Technology and Applications Competence Centre This developmental research project is commissioned by the Ministry of Social Affairs and carried out by the Software Technology and Applications Competence Centre (STACC), Quretec and University of Tartu from March to June 2015. The project is supported by the European Union Structural Funds via the programme TerVE implemented by the Estonian Research Council. Contact information: OÜ Tarkvara Tehnoloogia Arenduskeskus, Ülikooli 2 (5th floor), Tartu, Estonia; +372 740 7522, [email protected]. Information Architecture of Estonian Personalised Medicine Pilot Project iii Executive summary Since completion of the first sequence of human genome in 2003, followed by a rapid decline in costs of sequencing technologies on one hand and acquisition of deeper knowledge about the genome function on the other, we are nearly there to embrace genomic data as a cost-effective component of routine health service. Several personalised medicine initiatives have been launched all around the world in recent years. Amongst them is an Estonian pilot project for implementing personalised medicine in health care on national scale, planned to start in autumn 2015. This document summarises the preliminary analysis about the current state and future needs for information architecture and data management aspects related to the gradual implementation of the national personalised medicine initiative in Estonia. In the overview section a comprehensive description is given about the current components of the existing IT infrastructure laying ground for executing the principles of personalised medicine in Estonia. Remarkable amount of health data is available in databases online that can be linked together thanks to Personal Identification Codes and technological stack of Estonian IT infrastructure (X- Road). Tissue samples of 5% of the population are collected and 2400 of them will be soon fully sequenced. Several research groups have been working on data acquisition, extraction and quality as well as developing new decision support algorithms. However, all these approaches can be handled as ad hoc solutions and do not form a full closed cycle from research to treatment to follow-up and research again. The automatic decision support, the vital part of personalised medicine, even without the genetic component, has not been used in practice in Estonia as of today. We describe some key components and issues of information system and data management in the context of personalised medicine: linking the data, managing the consents, security and privacy. The Pilot Project shall seek the right balance between the possible lack and excess of privacy, because any leakage of highly sensitive genomic information could raise opposition against the whole project, but on the other hand, an excess of privacy-related hurdles could radically slow down research. It seems reasonable to divide general personalised medicine process into five sub-processes based on their nature: the clinical activities and direct interaction with the patient, managing big personalised data, decision support, pseudonymisation and research. We enlist the functional requirements together with possible solution alternatives for each of them. We also describe four different specific use cases across all these sub-processes. We also propose a four-stage strategy for building necessary information architecture by expanding the system step by step. During each stage it is still possible to execute the full cycle of the personalised medicine process. One should start applying personalised medicine principles on gene donors of the Estonian Biobank (EGCUT), and then move step by step to the whole Estonian population. International experts agree that it is now the right time to start applying personalised medicine principles as the sequencing costs are dropping and there are already some existing evidence-based cost-effective use cases to work with. However, the full detailed execution of the information architecture, data sharing, research and development will be highly dependent of the involved organisations and structures. Expertise exists in Estonia due to strong research universities and teams close to these on one hand and the appropriate information management on the other hand. There must be appropriate organisational decisions to strengthen the current expertise and future continued long-term growth and commitments on the national level. The main question boils down to the team(s) that will develop and execute (in an appropriate R&D setting) the various decision support systems required for the automated data-driven personalised approaches in medicine. Information Architecture of Estonian Personalised Medicine Pilot Project iv Lühikokkuvõte Alates inimgenoomi esmakordsest sekveneerimisest 2003. aastal on sekveneerimistehnoloogiate hind tänaseks väga kiiresti lan- genud, jõudes 1000C täisgenoomi ning 50C üle miljoni SNP genotüpiseerimise eest. Samal ajal on oluliselt kasvanud teadmised genoomi funktsioonidest, geenide seostest haiguste põhjustega või kaudsete riskide hindamisega. Täisgenoomide sekveneerimi- se hind jätkab avatud turul langust, kuid meie teadmised ja kogemused kasvavad. Seetõttu oleme nüüdseks jõudnud punkti, kus genoomika andmeid võiks hakata käsitlema rutiinse tervishoiuteenuse kulu-efektiivse komponendina. Viimastel aastatel on maailmas alustatud mitmeid erinevaid personaalmeditsiini projekte. Nende hulka kuulub ka Eesti perso- naalmeditsiini pilootprojekt, millega on plaanis alustada tervishoiusüsteemi tasemel katsetusi 2015. a sügisel. Eesti jaoks loob unikaalse eelise juba praegu olemasolev Eesti Geenivaramu andmekogu 50 000 geenidoonori andmete ning 2300 täisgenoomiga ning teiseks Eesti tervishoiuandmete kõrge digitaliseerituse ja tsentraliseerituse aste. Käesolev raport võtab kokku Eesti personaalmeditsiini pilootprojekti rakendamiseks vajaliku infoarhitektuuri ja andmehalduse het- keolukorra ning täiendavate vajaduste eelanalüüsi tulemused. Hetkeolukorra kirjeldus annab ülevaate olemasolevatest IT infrastruktuuri komponentidest. Märkimisväärne osa Eesti rahva tervise- andmetest on reaalaja andmebaasidest kättesaadav ja iga isiku andmed eri andmekogudes ühendatavad tänu isikukoodidele ja X-tee andmevahetuskihile. Eestis on tänaseks kogutud koeproovid 5% rahvastiku kohta, 2400 neist saavad peagi ülegenoomselt sekve- neeritud. Mitmed teadusgrupid on juba tegelenud andmete kogumise, eraldamise ja kvaliteedi uurimisega, samuti uute otsusetoe algoritmide väljatöötamisega. Sellegipoolest tuleb nimetatud tegevusi käsitleda pigem ad hoc lahendustena, kuna need ei moodusta veel terviklikku tsüklit teadus- ravi-jälgimine-teadus ahelas. Automaatset otsusetuge, mis on personaalmeditsiini oluline osa, ei ole Eesti praktikas tänaseni kasu- tatud, isegi mitte ilma geneetika komponendita. Ka maailmas ei ole valmis rakendataval kujul olemas kõikehõlmavaid automaatse otsusetoe rakendusi ega geneetika baasil tehtavate kõikvõimalike riskiskooride ja ennustusalgoritmide andmebaasi. Sellise algorit- mide andmebaasi ja otsusetoe rakenduste arendamine oleks Eestile unikaalne eelis ja rahvusvahelise koostöö võimalus. Käesolevas raportis kirjeldatakse mõningaid olulisemaid komponente ja probleeme personaalmeditsiini infoarhitektuuri ja andme- halduse kontekstis: eri andmekogudest andmete ühendamine nii teadus- ja rakendusuuringute kui otsusetoe tarbeks, informeeritud nõusolekute haldamine, turvalisus ja privaatsus. Pilootprojektis tuleb leida leida õige tasakaal vähese ja liiase privaatsuse tagamise mehhanismide vahel. Ühelt poolt võib mistahes genoomi info leke tekitada suurt vastuseisu kogu projektile. Teiselt poolt või- vad aga privaatsuse liigse kaitsega seotud takistused drastiliselt pidurdada teadustegevust, mis on pilootprojekti ja tuleviku arengu võtmekomponent. Uuringud on vajalikud nii otsusetoe algoritmide väljatöötamiseks kui rahvusvaheliste ravijuhiste ja algoritmide valideerimiseks Eesti andmetel enne juurutamist. Oma töös jagame personaalmeditsiini tervikprotsessi olemuslikult viieks alamtegevuseks: kliiniline tegevus ja vahetu suhtlemine patsiendiga, isikustatud suurandmete haldus, otsusetoe rakendused, andmete pseudonümiseerimine ja teadus- ning arendustege- vus. Toome välja nende tegevuste jaoks funktsionaalsed nõuded koos võimalike lahendusalternatiividega. Samuti kirjeldame nelja konkreetset kasutuslugu mis katavad neid alamprotsesse. Information Architecture of Estonian Personalised Medicine Pilot Project v Pakume välja neljasammulise strateegia vajaliku infoarhitektuuri loomiseks, kus süsteemi üldist võimekust laiendatakse iga sam- muga. Igal etapil on võimalik läbida kogu personaalmeditsiini protsessi tsükkel. Personaalmeditsiini printsiipide rakendamist alus- tatakse Eesti Geenivaramu doonorite peal ja seejärel laiendatakse lähenemist samm-sammult kogu Eesti elanikkonnale. Rahvusvahelised eksperdid nõustuvad, et just nüüd on õige aeg alustada personaalmeditsiini põhimõtete riiklikul
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