Patient centric portal

Patientcentricportal
Patientcentricpages
Enhanced Patientcentricpages
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Primaries
Recurrence
Multiple samplesforthesamepatient:spatial/temporaldynamics
Enhanced Patientcentricpages
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Multiple samplesforthesamepatient:spatial/temporaldynamics
Timeline
Primaries
Recurrence
Enhanced Patientcentricpages
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Primaries
Recurrence
Multiple samplesforthesamepatients:spatial/temporaldynamics
Enhanced Patientcentricpages
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Primaries
Recurrence
Example:Treatmenttimelineandassociatedgeneticchanges
Enhanced Patientcentricpages
• Annotateprivate
andsharedevents
• Primaryvs
recurrencedrivers
Enhanced Patientcentricpages
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Example:Treatmenttimelineandassociatedgeneticchanges
PSAfalling,thenrisingagain
cBioPortal forcancergenomics
• cBioPortal (multipledatasets)
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http://cbioportal.org/
Comprehensivetoolsfordataexplorationandintegration
Mostextensiveresourceforcancergenomicsprojects
Greatfeatureselectionforgene-basedqueries
Limitedfeatureselectionforpatient-basedqueries
Fromquerypageyoucandownloadquerydownloads
FromDataSetsyoucandownloadallfilesforastudy
• Nocrossstudy
• Nodataselection
• Toolsfordatadisplay:Oncoprinter /MutationMapper
• SystematicaccessthroughR/MATLABlibraries
cBioPortal forcancergenomics
cBioPortal forcancergenomics
AppliedCancerGenomics
• JournalClub1
• UsethecBioPortal toexplorethisdataset
AppliedCancerGenomics
• JournalClub2
• UsethecBioPortal toexplorethisdataset
TheCancerCellLineEncyclopedia(CCLE)
CCLE
• Prettybadfordataexploration
• Provide flatfilesfordownload (YOUNEEDTO
REGISTER)
UsingIGVtoexplorecopynumberdata
• DownloadthesegmentationfilefromtheCCLPwebsite(orgetitfrom
thecoursewebsite)
• DownloadIGV
• VisualizeCCLEsegmenteddata
• Retrievecelllineannotations
• CreateannotationfileforIGVinR(columnsubsetting)
• LoadannotationsinIGV
UsingIGVtoexplorecopynumberdata
• CreateannotationfileforIGVinR(columnsub-setting)
ccle = read.table("CCLE_sample_info_file_2012-10-18.txt",header=T,sep="\t")
ccle.sub = ccle[,c("CCLE.name","Site.Primary")]
colnames(ccle.sub) = c("cell.line","type")
write.table(ccle.sub,file="ccle_annotations.txt",sep="\t",col.names=TRUE,
row.names=FALSE,quote=F)
CCLE
• https://portals.broadinstitute.org/ccle/home
• Notreallygoodtoexploregenomicdataoncelllines,betterusethecBioPortal forthis
• Theymaintainhoweveralltheflatfilesforthecollection
• http://www.cbioportal.org/study?id=cellline_ccle_broad#summary
• Hereisthelinktotheportal
• Nodrugdataavailable
TheCOSMICCellLineProject(CCLP)
TheCOSMICCellLineProject(CCLP)
TheCOSMICCellLineProject(CCLP)
TheCOSMICCellLineProject(CCLP)
TheCOSMICCellLineProject(CCLP)
TheCOSMICCellLineProject(CCLP)
TheCOSMICCellLineProject(CCLP)
TheCOSMICCellLineProject(CCLP)
Celllinespecificpageallowtobrowse/query allvariantsforagivenline
TheCOSMICCellLineProject(CCLP)
TheCOSMICCellLineProject(CCLP)
(you mayfind referenceintheliteraturetoGDSC dataset– samething butspecificallyreferring todrugscreening data)
TheCOSMICCellLineProject(CCLP)
• CelllinesrankedbyIC50
• IC50valueshasbeen
interpolated/predicted
startingfrommeasured
ones
• IC50in“red”arepredicted
abovethemaximumdose
tested(“resistantlines”)
Features
associatedwith
Sensitivity
Features
associatedwith
Resistance
• Rankcelllinesforaspecific
tissue
TheCOSMICCellLineProject(CCLP)
(you mayfind referenceintheliteraturetoGDSC dataset– samething butspecificallyreferring todrugscreening data)
CCLP
• http://cancer.sanger.ac.uk/cell_lines
• Generalsearchquerybox:searchforgenecanthenleadtocelllineswithmutationinthe
gene (againonegeneatatime)
• PotentiallyinterestinguseofCancerBrowsertoselectmodelsbasedontissueandsubtissue
• TheGenomebrowserallowsyoutoqueryagene- look-upspecificmutations– findsamples
withit
• Baddataintegration
• Downloadisprettygood
• Drugsensitivityisprettygoodtoo,butalsoquiteconfusing– multiplesteptoextractbasic
information
• E.g.CNAfeaturesarereportedascodes– noideaofwhattypeandwhere
• UnfortunatelynotyetoncBioPortal
PDXModelSearch(JacksonLaboratory– MTB)
PDXModelSearch(JacksonLaboratory– MTB)
PDXModelSearch(JacksonLaboratory– MTB)
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Download fullsetofmutations
GeneExpressionlevels
Copynumber variants
(Notalltheseinformation arealwaysavailable)
PDXModelSearch(JacksonLaboratory– MTB)
PDXportal(MTB)
• http://tumor.informatics.jax.org/mtbwi/pdxSearch.do
• PDXcollectiondatabase– searchbygenealteration
• Onegeneatthetimeunfortunatelyinthesearch,butinterestingfirststep
• Theyhavemodelspecificpagewithallvariants/RNA-seq /CNV(notalldatatypeforall
models)
• Notclearwhether,variantsaresomaticonly,suspecttheyareall
• http://tumor.informatics.jax.org/mtbwi/facetedSearch.do?start=0
• Theyalsomaintaindatabaseofgenomicallycharacterizedmousemodels