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

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An MIABIS based Electronic Biosample Registry at the Medical University of Innsbruck Philipp&Hofer a ,"Heidi"Fiegl b ,"Jus-na"Angerer b ,"Elisabeth"Mueller7 Holzner b ,"Mar-na"Chamson b

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An MIABIS based Electronic Biosample Registry at the Medical University of Innsbruck

Philipp&Hofer¹a,"Heidi"Fieglb,"Jus-na"Angererb,"Elisabeth"Mueller7 Holznerb,"Mar-na"Chamsonb,"Helmut"Klockerc,"Eberhardt"Steinerc,"Helga Hauffec,"Johannes"Zschocked,"and"Georg"Goebela

1philipp.hofer@i+med.ac.at

aDepartment"of"Medical"Sta-s-cs,"Informa-cs"and"Health"Economics,

Innsbruck7Medical7University

bDepartment7of7Obstetrics7and7Gynecology,7Innsbruck7Medical7University cDepartment7of7Urology,7Innsbruck7Medical7University dDivision7of7Human7GeneBcs,7Innsbruck7Medical7University

'

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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

& &

2 philipp.hofer@i,med.ac.at/MIE2014

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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

3 philipp.hofer@i,med.ac.at/MIE2014

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philipp.hofer@i+med.ac.at/MIE2014

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

4 philipp.hofer@i+med.ac.at/MIE2014

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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 , ,

5 philipp.hofer@iDmed.ac.at/MIE2014

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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

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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.

(

7 philipp.hofer@iDmed.ac.at/MIE2014

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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

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Result:(Iden,fica,on(of(SOP’s(for Tissue(and(Body(Fluid(Samples((e.g. Serum)

9

Department Collec-on Container Processing (centrifuga-on) Storage Temperatur e Sample Labeling Gynecology<& Obstetrics

Tubes with separator gel 10 min., 2.500 x g, RT

  • 50°C

Barcode label

Urology

Tubes with separator gel 10 min., 2.000 x g, RT

  • 80°C

Barcode label

Clinical<Neurology

Tubes w/o separator gel 10 min., 1.300 x g, RT

  • 20°C

manual

Dermatology

Tubes w/o separator gel 10 min., 1.000 x g, 20°C

  • 20°C

manual

Internal<Medicine I

Tubes with separator gel 15 min., 1.200 x g, 20°C

  • 80°C

manual

Internal<Medicine II

Tubes with separator gel 15 min, 2.000 x g, 15°C

  • 80°C

Barcode label

Internal<Medicine V

Tubes with separator gel 15 min, 2.000 x g, 15°C

  • 80°C

manual

philipp.hofer@i,med.ac.at/MIE2014

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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

(

10

(

philipp.hofer@i-med.ac.at/MIE2014

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Use$case$2$(search$result):$

Get$exis3ng$sample$collec3ons$containing$sample$sets$with$ICD10 diagnosis$„C54.1$Malignant$neoplasm$of$endometrium“

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$

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Extended'MIABIS'Data'Model

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Material*Type Serum Number*of*Samples 400 Aliquots/Blocks 3 Amount 3*ml Storage Temperature A50°C Sample*Handling 10*min.,*2,500*x*g, RT Diagnosis C54.1*:*Malignant neoplasm*of endometrium Container Tubes*with separator*gel

  • Based'on'a'subset'of'the

MIABIS'2.0'model3 '

  • Minimum'Informa>on'About

Biobank'data'Sharing

  • Sample'collec>on'informa>on

at'aggregate'level '

  • Defini>on'of'one'sample

collec>on'with'several'contact persons'for'each'department '

  • Sample'collec>ons'comprise

several'sample'sets '

[3]*Loreana*Norlin,*M.Sc,*A*Minimum*Data*Set*for*Sharing*Biobank*Samples,*InformaSon,*and*Data:*MIABIS.,*BiopreservaSon*and*Biobanking, August*2012,*10(4):*343A348

philipp.hofer@iAmed.ac.at/MIE2014

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philipp.hofer@i+med.ac.at/MIE2014

Extended'MIABIS'Data'Model

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  • Web'applica7on

– PHP'based Symphony'MVC framework '

  • Backend:

– Apache'web'server – MYSQL'database server

Contact ICD10_Diagnosis Samples DataCategory Country SampleCollec7on Juris7cPerson

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philipp.hofer@i+med.ac.at/MIE2014

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

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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 ,

15 philipp.hofer@iNmed.ac.at/MIE2014

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Thank&you&for&your&a,en.on&!

16

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 Department#for#Medical#Sta3s3cs, Informa3cs#and#Health#Economics Medical#University#of#Innsbruck Philipp.Hofer@i>med.ac.at #

philipp.hofer@i>med.ac.at/MIE2014

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Thank&you&for&your&a,en.on&!

17

Workgroup:)MUI)Biobank DDr.&Johannes&Zschocke,&Department&of&Human&Gene9cs Mag.&Dr.&Georg&Goebel,&Department&of&Medical&Informa9cs, Sta9s9cs&and&Health&Economy Dr.&Heidelinde&Fiegl,&Department&of&Gynecology&and&Obstetrics Dr.&Helmut&Klocker,&Department&of&Urology Dipl.Ing.&Sabrina&Neururer,&Department&of&Medical&Informa9cs, Sta9s9cs&and&Health&Economy Philipp&Hofer&MSc.,&Department&of&Medical&Informa9cs,&Sta9s9cs and&Health&Economy Medical&University&of&Innsbruck Philipp)Hofer Department&for&Medical&Sta9s9cs, Informa9cs&and&Health&Economics Medical&University&of&Innsbruck Philipp.Hofer@iLmed.ac.at Thanks)to)following)persons)for)help)and)support Dr.&Heidelinde&Fiegl,&Department&of&Gynecology&and&Obstetrics Dr.&Elisabeth&MuellerLHolzner,&Department&of&Gynecology&and&Obstetrics Mag.&Mar9na&Chamson,&Department&of&Gynecology&and&Obstetrics Dr.&Jus9na&Angerer,&Department&of&Gynecology&and&Obstetrics Dr.&Helmut&Klocker,&Department&of&Urology Mag.&Helga&Hauffe,&Department&of&Urology Mag.&Eberhardt&Steiner,&Department&of&Urology Medical&University&of&Innsbruck

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4.2$Use$Cases$I

$

  • Example:$Get$exis5ng$sample$collec5ons$containing$sample

sets$with$ICD10$diagnosis$„C54.1$Malignant$neoplasm$of endometrium“ $

  • The$biosample$register$contains$no$informa5on$on$individual

samples $

  • It$is$expected$that$such$queries$will$be$also$handled$by$a

future$biobank$soMware $

  • Nevertheless,$it$serves$as$a$basis$for$a$func5onal$metadata

interface$for$future$biobank$soMware $ $

18 philipp.hofer@i-med.ac.at/MIE2014

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3.2$Example$of$3$LGM:$Data$flow$at the$Department$of$Urology

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Domain$layer:$Business funcAons,$e.g. documentaAon$of samples$and$clinical$data related $ Logical$layer:$SoEware components,$e.g.$sample management$system $ Physical$layer:$Hardware components,$e.g.$Server

philipp.hofer@i-med.ac.at/MIE2014