The BDDS Platform for Big Biomedical Data Management and Analysis: Discovering the role of Amyloid Deposition in Neurodegenerative Diseases

Ravi K Madduri, Michael D’Arcy, Kyle Chard, Alexis Rodriguez, Judy Pa, Naveen Ashish, Ben Heavner, Gustavo Glusman, Ivo Dinov, John Van Horn, Eric Deutsch, Nathan Price, Leroy Hood, Carl Kesselman, Ian Foster, Joseph Ames, Arthur Toga

University of Chicago, University of Southern California, Institute for Systems Biology, University of Michigan

Abstract

Approach

The BDDS Platform Analyzing role of Amyloid Burden

Discussion & Conclusions

Bibliography

Objective:Investigateiftherearecommonalitiesinpatternsofamyloiddeposition inindividualswithAlzheimer’sDiseaseorParkinson’sDiseasethatidentifythoseindividualswithoratriskforcognitivedysfunctionApproach:Wecreatedaplatform forintegrationofmulti-omic data,facilitatedatadiscovery,cohortcreation, enablerapid,scalableandreproducible analysisandfinallypublishresults

Weemployedasystematic,reproducibleapproachthatleveragedexistingcapabilitiesforunderstandingcommonalitiesinamyloiddepositionthatincludedthefollowingstagesandchallenges

1.DataIngest- ERMRest• Phenotypic,Genotypicand

Imagingdatasets• Multiplerepositories• DataUsageAgreements• Automateddatacleanupand

ingest

2.DataQueryandExchange- BagIt• ERMRest provideshigh-levelAPI

forquery• AdoptedtheBagIt specification

tocreatedatabags• EnhancedBagIt tosupportbig

biomedicaldata3.DataAnalysis– PipelineandGlobusGenomics• LONIPipelinerunstheanalysis

ontheamyloidPETandMRIimagesandoutputsamyloidindexvalues(SUVR:standarduptakevalueratio)foreachbrainregion,foreachsubjectusingcomputationalresourcesatUSC

• GenomicsanalysisusingGlobusGenomicsontheAmazoncloud

• Leverageselasticprovisioner thatoptimizesperformanceandcosts

4.DataPublicationandIntegration– GlobusPublicationandERMRest• Resultsfromanalysisare

integratedwithERMRest• ResultsarepublishedinGlobus

Publicationservicewithappropriatemetadata

• Multi-omic data• Multipledistributedrepositories• Data usage agreements• Data cleanup and integration

DataIngest

• Easy tofinddata• Enable creation ofpatient cohorts• Send data foranalysis

DataQueryandExchange

•Multipleanalysisplatforms• Ease ofuse• Scale

DataAnalysis

• Enable discovery• End-to-end data view

DataPublication

andIntegration

Images f r om Alzheim er 's andPar kinson's

1. TheBagIt FilePackagingFormat(V0.97)availableat:http://tools.ietf.org/html/draft-kunze-bagit-11

2. Minids:http://minid.bd2k.org

SUVR values forcortical gray matterregions of interestoverlaid onas tructural MRI for as inglesubject

Exom esandwholegenom es f r om Alzheim er 's andPar kinson'sPhenot ypic dat a

• Wecreatedapowerfulplatformbyintegratingseveralexistingservicesandcapabilities

• PlatformdevelopmentresultedinadoptingandextendingBagIt formatforbiomedicalbigdata

• FutureworkincludesapplyingtheplatformforanalyzingAlzheimer’sdata

• ReferenceimplementationoftheNIHCommons

ark:/88120/r83w2c