update on wp1: tools and methods for high -throughput ... · assessment, visualization and so on....
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Junyan Lu2017Nov.,Heidelberg
Update on WP1:Tools and methods for high-throughput perturbation assays and integrative analysis
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Primarylymphomacells
(CLL,AML,BL…)
Project design
Transcriptome Metabolism
DNASequencing Methylome SNParray
ClinicaldataDrugresponse
Multi-omicsprofilingofbloodcancerpatients
Clinicaltranslation
Integrativedataanalysis
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Datagatheredin2017:Ø EMBLscreen(408compoundson135patientsamples)Ø CPS1000:(64compoundson732patientsamples)Ø AdditionalRNAseq dataon29patientsamplesØ AdditionalWGSdataon88patientsamples
Multi-omicsdatasets(summarizedin2016)
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Challenges
• Datamanagement
• Standardizeddataprocessing
• Datavisualizationandsharing
• Integrativeanalysis
AimsofWP1:
Ø Tacklingaboveproblemsbydesignamodular,end-to-endchainoftoolstoperformfirst-lineanalysistasks,includingdataimport,metadatamanagement,qualityassessment,visualizationandsoon.
Ø Developnovelintegrativeanalysestoolsandapplyingthemtopersonalizedmedicinestudies.
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Outline• Introduction
• Tools and platforms
ØData management
ØPipeline for high-throughput perturbation data analysis
ØTools for integrative multi-omics analysis
• Application on biological questions
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P0004
15PB0111
12PB0042
Aliquot1
Aliquot1
Aliquot1
+
Patients Samples Aliquots Multi-omicsdata
Datamanagement
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patientsample aliquotdiagnosis
project
aliquotused
tumorbankCopy
RMySQLpackageTumorbank
(Accessdatabase)
Jennifer Huellein
Relationaldatabaseforsamplemanagement
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http://mozi.embl.de/patientExplorer/
Shinyappforvisualizingsampleandpatientinformation
Jennifer Huellein
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Ex-vivodrugscreening
Rpackagefordatastorageandintegration
drugScreenExplorertidyverse
RNAsequencing
STARHTSeqDESeq2
Clinicaldata
RMySQLShiny
… …
PrimaryBloodCancerCellEncyclopedia(PACE):
Multi-omicsdatasets(before2016),PACE2.0isontheway.
Functionsforquery,transformationandplotting
Datapackage
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Rawdataprocessing Qualityassessment
Postprocessing Report Visualization
andsharing
PlateReader:Envision
Pipelineforhigh-throughputperturbationdataanalysis
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Rawmeasurement(txtformat)
readPlate()toreadrawdataforeachplate
Step1.Dataimport
sampleannotationfile(csvfile)
platelayoutfile(csvfile)
readScreen()
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StrictlyStandardizedMeanDifference(SSMD)
Step2.Qualityassessmentrawsignaldistribution
PCAplot
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conc.[µM]
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48ABC 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 1 25 14 38 14 38 14 38 14 38 14 38 14 38 14 38 14 38 14 38 14 38 14 38D 49 73 49 73 49 73 49 73 49 73 49 73 49 73 49 73 49 73 49 73 49 73 62 86 62 86 62 86 62 86 62 86 62 86 62 86 62 86 62 86 62 86 62 86E 2 26 2 26 2 26 2 26 2 26 2 26 2 26 2 26 2 26 2 26 2 26 15 39 15 39 15 39 15 39 15 39 15 39 15 39 15 39 15 39 15 39 15 39F 50 74 50 74 50 74 50 74 50 74 50 74 50 74 50 74 50 74 50 74 50 74 63 87 63 87 63 87 63 87 63 87 63 87 63 87 63 87 63 87 63 87 63 87G 3 27 3 27 3 27 3 27 3 27 3 27 3 27 3 27 3 27 3 27 3 27 16 40 16 40 16 40 16 40 16 40 16 40 16 40 16 40 16 40 16 40 16 40H 51 75 51 75 51 75 51 75 51 75 51 75 51 75 51 75 51 75 51 75 51 75 64 88 64 88 64 88 64 88 64 88 64 88 64 88 64 88 64 88 64 88 64 88I 4 28 4 28 4 28 4 28 4 28 4 28 4 28 4 28 4 28 4 28 4 28 17 41 17 41 17 41 17 41 17 41 17 41 17 41 17 41 17 41 17 41 17 41J 52 76 52 76 52 76 52 76 52 76 52 76 52 76 52 76 52 76 52 76 52 76 65 89 65 89 65 89 65 89 65 89 65 89 65 89 65 89 65 89 65 89 65 89K 5 29 5 29 5 29 5 29 5 29 5 29 5 29 5 29 5 29 5 29 5 29 18 42 18 42 18 42 18 42 18 42 18 42 18 42 18 42 18 42 18 42 18 42L 53 77 53 77 53 77 53 77 53 77 53 77 53 77 53 77 53 77 53 77 53 77 66 90 66 90 66 90 66 90 66 90 66 90 66 90 66 90 66 90 66 90 66 90M 6 30 6 30 6 30 6 30 6 30 6 30 6 30 6 30 6 30 6 30 6 30 19 43 19 43 19 43 19 43 19 43 19 43 19 43 19 43 19 43 19 43 19 43N 54 78 54 78 54 78 54 78 54 78 54 78 54 78 54 78 54 78 54 78 54 78 67 91 67 91 67 91 67 91 67 91 67 91 67 91 67 91 67 91 67 91 67 91O 7 31 7 31 7 31 7 31 7 31 7 31 7 31 7 31 7 31 7 31 7 31P 55 79 55 79 55 79 55 79 55 79 55 79 55 79 55 79 55 79 55 79 55 79Q 8 32 8 32 8 32 8 32 8 32 8 32 8 32 8 32 8 32 8 32 8 32R 56 80 56 80 56 80 56 80 56 80 56 80 56 80 56 80 56 80 56 80 56 80S 9 33 9 33 9 33 9 33 9 33 9 33 9 33 9 33 9 33 9 33 9 33 20 44 20 44 20 44 20 44 20 44 20 44 20 44 20 44 20 44 20 44 20 44T 57 81 57 81 57 81 57 81 57 81 57 81 57 81 57 81 57 81 57 81 57 81 68 92 68 92 68 92 68 92 68 92 68 92 68 92 68 92 68 92 68 92 68 92U 10 34 10 34 10 34 10 34 10 34 10 34 10 34 10 34 10 34 10 34 10 34 21 45 21 45 21 45 21 45 21 45 21 45 21 45 21 45 21 45 21 45 21 45V 58 82 58 82 58 82 58 82 58 82 58 82 58 82 58 82 58 82 58 82 58 82 69 93 69 93 69 93 69 93 69 93 69 93 69 93 69 93 69 93 69 93 69 93W 11 35 11 35 11 35 11 35 11 35 11 35 11 35 11 35 11 35 11 35 11 35 22 46 22 46 22 46 22 46 22 46 22 46 22 46 22 46 22 46 22 46 22 46X 59 83 59 83 59 83 59 83 59 83 59 83 59 83 59 83 59 83 59 83 59 83 70 94 70 94 70 94 70 94 70 94 70 94 70 94 70 94 70 94 70 94 70 94Y 12 36 12 36 12 36 12 36 12 36 12 36 12 36 12 36 12 36 12 36 12 36 23 47 23 47 23 47 23 47 23 47 23 47 23 47 23 47 23 47 23 47 23 47Z 60 84 60 84 60 84 60 84 60 84 60 84 60 84 60 84 60 84 60 84 60 84 71 95 71 95 71 95 71 95 71 95 71 95 71 95 71 95 71 95 71 95 71 95
AA 13 37 13 37 13 37 13 37 13 37 13 37 13 37 13 37 13 37 13 37 13 37 24 48 24 48 24 48 24 48 24 48 24 48 24 48 24 48 24 48 24 48 24 48AB 61 85 61 85 61 85 61 85 61 85 61 85 61 85 61 85 61 85 61 85 61 85 72 96 72 96 72 96 72 96 72 96 72 96 72 96 72 96 72 96 72 96 72 96AC S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2AD S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S1 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2 S2AFAG
1 compoundnumberS1 Standard1=190001:03S2 Standard2=190004:03
negativecontrol DMSOinwaterpositivecontrol 30µMDanorubicinin0.3%DMSO/water
poitiveco
ntrol
0.0015 0.0005
water
negativecontrol
negativecontrol
30 10 3.3333 1.1111 0.3704 0.1235 0.0412 0.0137 0.0046 0.0015 0.0005 30 10 3.3333 1.1111 0.3704 0.1235 0.0412 0.0137 0.0046
PlatelayoutforEMBL2016screen idealresults
highnoiseplate edgeeffect
Step2.Qualityassessment
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Edgeeffectcorrectionbasedonlocalregression
Step3.Post-processing
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Normalizedcounts
”defacto”negativecontrols(dmso,PBS,drugswithlowestconcentrations)
Estimatededgeeffect
Applycorrectionbysubstracting background
2DLOESS
span=1
ForCPS1000(384-wellplate)
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Beforeco
rrectio
n
rowwise columnwise
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Venetoclax
Panobinostat
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Normalizedcounts
”defacto”negativecontrols(dmso,water,empty,drugswith
lowestconcentrations)
2DLOESS
Estimatededgeeffect
Applycorrection
ForEMBL2016(1536well-plate)
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“2D2-tail”sigmoidmodel
surfacefitby2DLOESS
Anewmethodforestimatingedgeeffect
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Edgeeffectcorrectionresults
Beforecorrelction Estimatededgeeffect Estimatededgeeffect
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Ø Percentinhibitionateachconcentration(normalizedbyinnernegativecontrols)
Ø IC50curvesandAUC(by”drc”package)
Ø Averageoverall(orselected)concentrations
Step4.Summarization
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Ex-vivodrugscreening:EMBL2016CPS1000…
multi-omicsdata
Step5.Sharingandvisualization
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http://mozi.embl.de/drugScreens/
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MOFA-- MultiOmics FactorAnalysis(unsupervised)
BrittaVelten
Toolsforintegrativemulti-omicsanalysis
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SummaryØA SQL and Shiny based platform has been developed for patient
sample management.
ØA streamlined pipeline for the processing, quality control and visualizing of high-throughput perturbation assay has been developed.
ØComputational tools for integrative multi-omics analysis are made.
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Next step:
Ø Automization and generalization
Ø Integration of multiple tools and platforms
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Outline• Introduction
• Tools and platforms
ØData management
ØPipeline for high-throughput perturbation data analysis
ØTools for integrative multi-omics analysis
• Application on biological questions
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1.DrugPerturbationBasedStratificationofBloodCancer
Ø Drugresponsesaremodulatedbynumerousgeneticvariantsinbloodcancers
Ø Bloodcancerpatientscanbestratifiedbytheirdifferentialdrugresponses,whichreflectsunderlyingpathwayactivities
(Dietrich,Oleś andLuetal.,manuscriptaccepted)
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Acknowledgement
ThorstenZenz
MichelleLibério
SebastianScheinost
WolfgangHuberGroup
ChemicalBiologyCoreFacility
Sascha Dietrich
SophieRabe
KerstinPutzker JoeLewis