An MIABIS based Electronic Biosample Registry at the Medical - PDF document

An MIABIS based Electronic Biosample Registry at the Medical University of Innsbruck Philipp&Hofer ¹a ,"Heidi"Fiegl b ,"Jus-na"Angerer b ,"Elisabeth"Mueller7 Holzner b ,"Mar-na"Chamson b ,"Helmut"Klocker c ,"Eberhardt"Steiner c ,"Helga Hauffe c ,"Johannes"Zschocke d ,"and"Georg"Goebel a 1 philipp.hofer@i+med.ac.at a Department"of"Medical"Sta-s-cs,"Informa-cs"and"Health"Economics, Innsbruck7Medical7University b Department7of7Obstetrics7and7Gynecology,7Innsbruck7Medical7University c Department7of7Urology,7Innsbruck7Medical7University d Division7of7Human7GeneBcs,7Innsbruck7Medical7University '

Table&of&Contents Background&&&Aim&of&the&project Innsbruck&University&Hospital BBMRI.AT Impact&of&InformaCon&about&Samples & Results Sample&CollecCons Sample&Management&Tools IdenCficaCon&of&SOP’s&for&Tissue&and&Body&Fluid&Samples Use&Cases&Concerning&Queries&IdenCfied Extended&MIABIS&Data&Model & Discussion&and&Outlook & & philipp.hofer@i,med.ac.at/MIE2014 2

Aims%of%the%local%BBMRI%Project 1. Iden9fica9on%of%exis9ng%local%biosample%collec9ons 2. Analysis%of%exis9ng%standard%opera9ng%procedures%(SOP’s) 3. Iden9fica9on%of%sample%management%systems%in%use 4. Defini9on%of%use%cases 5. Concept%of%a%minimum%data%model%and%pilot%implementa9on philipp.hofer@i,med.ac.at/MIE2014 3

Innsbruck)University)Hospital • Organiza9on – 38<clinical<departments,<1,600<beds – Medical<theory<&<service<faciliEes:<9<departments • 3,000)medical)students • 1,800)employees,)330)researchers)and)clinicians • Most)important)medical)research)and)training)facility)in)the)western)part)of)Austria philipp.hofer@i+med.ac.at/MIE2014 philipp.hofer@i+med.ac.at/MIE2014 4

Background:,BBMRI.AT • BBMRI.AT:, Biobanking,and,Biomolecular,Resources,Research Infrastructure,=,Austrian,node , • Objec@ve,of,BBMRI.AT:, Integra@on,of,exis@ng,biosample,collec@ons,into,a na@onal,(Austrian),research,infrastructure , BBMRI.AT,–,Austrian,Members – 3#Medical#Universi0es: Graz#(lead),#Vienna,#Innsbruck – 3#other#Universi0es , • Objec@ve,of,BBMRI,(EU,level):, Integra@on,of,exis@ng,biosample,collec@ons,into an,European=wide,research,infrastructure , , philipp.hofer@iDmed.ac.at/MIE2014 5

Biobanks:* Impact*of*Informa2on*about*Samples Biobank*sample*informa2on*are*essen2al*for*clinical*research*outcomes1 – Poor%biospecimen%quality%may%lead%to%inaccurate%data%published%in%scien6fic%papers%2 – Delays%in%transport%may%explain%why%DNA%or%RNA%can%be%degraded3 – Shorter%or%longer%fixa6on%6mes%of%6ssue%either%influence%degrada6on%of%enzymes%or nucleic%acids3 * Imortant*quality*indicators*of*samples – PreEanaly6cal%processing%data – Long%term%storage%data – Availability%of%clinical%data * * * [1]%SimeonEDubach,%BeMer%Provenance%for%Biobank%Sample,%Nature%475%(2011),%454E455 [2]%SimeonEDubach,%Quality%really%maMers:%The%need%to%improve%specimen%quality%in%biomedical%research,%%J%Path%228%(2012),%431E433 [3]%Groenen%P%et%al.,%Preparing%pathology%for%personalized%medicine:%possibili6es%for%improvement%of%the%%%% %%%%%preEanaly6cal%phase,%Histopathology%59%(2011),%1E7 philipp.hofer@iEmed.ac.at/MIE2014 6

Results:(Sample(Collec0ons ! • 50(diseases7oriented(biosample(collec0ons(with(~(479,000(samples – collected!con*nuously!during!disease!courses – fresh!frozen!*ssue,!formalin!fixed!paraffin!embedded!materials,!serum,!plasma,!etc.) ( • 10.000(anonymized(blood(and(DNA(samples(of(rare(diseases ( • Sample(collec0ons(are(physically(distributed(in(12(different(departments ( • Informa0on(on(biosample(collec0ons(are(currently(not(visible(to(other departments(or(extramural(ins0tu0ons ( • Clinical(informa0on(available(for(most(samples – !via!the!hospital!informa*on!system – formalized!access!procedures:!Ethics!commiAee!etc. ( philipp.hofer@iDmed.ac.at/MIE2014 7

Results:(Sample(Management(Tools Department Serum Buffy.coat Plasma Ascites Urine Gynecology PGS-IT PGS-IT Urology Filemaker Filemaker Filemaker Filemaker Psychiatry Kaleida-Graph Word Neurology MS Access Dermatology PGS-IT Internal Medicine I MS Excel MS Excel Internal Medicine II PGS-IT PGS-IT Internal Medicine V MS Excel MS Excel MS Excel MS Excel Internal Medicine VI MS Excel MS Excel MS Excel MS Excel philipp.hofer@i,med.ac.at/MIE2014 8

Result:(Iden,fica,on(of(SOP’s(for Tissue(and(Body(Fluid(Samples((e.g. Serum) Storage Collec-on Processing Sample Department Temperatur Container (centrifuga-on) Labeling e Gynecology<& Tubes with 10 min., 2.500 x g, -50°C Barcode label Obstetrics separator gel RT Tubes with 10 min., 2.000 x g, Urology -80°C Barcode label separator gel RT Tubes w/o 10 min., 1.300 x g, Clinical<Neurology -20°C manual separator gel RT Tubes w/o 10 min., 1.000 x g, Dermatology -20°C manual separator gel 20°C Internal<Medicine Tubes with 15 min., 1.200 x g, -80°C manual I separator gel 20°C Internal<Medicine Tubes with 15 min, 2.000 x g, -80°C Barcode label II separator gel 15°C Internal<Medicine Tubes with 15 min, 2.000 x g, -80°C manual V separator gel 15°C philipp.hofer@i,med.ac.at/MIE2014 9

Result:(Use(Cases(Concerning Queries(Iden5fied((Examples) 1. Retrieve(all(collec5ons(of(body(fluids(at(the(Department(of(Gynecology ( 2. Get(exis5ng(sample(collec5ons(containing(sample(sets(with(ICD10(diagnosis „C54.1(Malignant(neoplasm(of(endometrium“ ( ( 3. How(many(collec5ons(with(more(than(1000(samples(exist(at(the(department(of Urology(? ( 4. Get(all(collec5ons(of(fresh(frozen(5ssues(or(FFPE(5ssue(samples(from(the prostate ( philipp.hofer@i-med.ac.at/MIE2014 10

Use$case$2$(search$result):$ Get$exis3ng$sample$collec3ons$containing$sample$sets$with$ICD10 diagnosis$„C54.1$Malignant$neoplasm$of$endometrium“ $ philipp.hofer@i,med.ac.at/MIE2014 11

Extended'MIABIS'Data'Model Material*Type Serum • Based'on'a'subset'of'the MIABIS'2.0'model3 Number*of*Samples 400 ' Aliquots/Blocks 3 Amount 3*ml • Minimum'Informa>on'About Biobank'data'Sharing Storage A50°C Temperature • Sample'collec>on'informa>on 10*min.,*2,500*x*g, at'aggregate'level Sample*Handling RT ' C54.1*:*Malignant • Defini>on'of'one'sample Diagnosis neoplasm*of endometrium collec>on'with'several'contact persons'for'each'department Tubes*with Container separator* gel ' • Sample'collec>ons'comprise [3]*Loreana*Norlin,*M.Sc,*A*Minimum*Data*Set*for*Sharing*Biobank*Samples,*InformaSon,*and*Data:*MIABIS.,*BiopreservaSon*and*Biobanking, several'sample'sets August*2012,*10(4):*343A348 philipp.hofer@iAmed.ac.at/MIE2014 12 '

Extended'MIABIS'Data'Model Samples SampleCollec7on • Web'applica7on – PHP'based Symphony'MVC framework ' • Backend: – Apache'web'server – MYSQL'database DataCategory server Contact Juris7cPerson ICD10_Diagnosis Country philipp.hofer@i+med.ac.at/MIE2014 13

Architecture:* Pilot:Implementa<on:of:Biobank Registry • Rela/onal*database*containing MIABIS*data*elements * • RDF*based*transmission*of collec/on*data*to: – Na<onal:Registry:(BBMRI.AT) – European:Registry:(BBMRI+ERIC) * • Exchange*of*aggregated*sample collec/on*data*between*the local*Biosample*Registry*and*a (upcoming)*hospitalEwide biobank*soGware philipp.hofer@i+med.ac.at/MIE2014 14

Discussion(and(Outlook Pros • Structured,informa2on,overview,about,stored,samples,and,SOPs,used • The,data,and,the,data,structure,obtained,from,the,sample,collec2on,analysis,showed,that MIABIS,as,a,common,descrip2on,model,is,useful • The,MUI,Biosample,Registry,enables,access,to,(manually),aggregated,informa2on,about exis2ng,internal,biosample,collec2ons • The,registry,provides,prerequisites,for,the,specifica2on,of,biobank,soIware,(data,model,,use cases,etc.) , Challenges • ICDN10,diagnosis,code,does,not,cover,the,full,index,of,rare,diseases >>,addi2onal,usage,of,the,Human,Phenotype,Ontology,(HPO)? • Informa2on,on,individual,samples,currently,not,available >>,biobank,BBMRI,soIware? • Automated,aggrega2on,of,metadata,about,individual,samples,on,collec2on,level >>,interface,design , philipp.hofer@iNmed.ac.at/MIE2014 15

Thank&you&for&your&a,en.on&! Philipp'Hofer Department#for#Medical#Sta3s3cs, Informa3cs#and#Health#Economics Medical#University#of#Innsbruck Philipp.Hofer@i>med.ac.at Thanks'to'following'persons # Georg#Goebel Sabrina#Neururer # Jus3na#Angerer Mar3na#Chamson # Heidelinde#Fiegl Elisabeth#Mueller>Holzner # Helga#Hauffe Helmut#Klocker Eberhardt#Steiner # Johannes#Zschocke # philipp.hofer@i>med.ac.at/MIE2014 16