Research in Progress April 2014
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The Genetic Signature of Behavior
Vanessa SochatResearch in Progress
April 1, 2014
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Autism Spectrum Disorders (ASD)
• $126 billion annually• ~1% prevalence
Social deficitsCommunication deficitsRepetitive behaviors
ASD
anxiety
PTSD
depression
autism
ADHD
bipolar
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What causes Autism Spectrum Disorders?
Neuroimaging
Environment
Behavior
Genetics 37% heritableMZ twins: 66% concordance, fraternel, 30%No single SNP genome-wide significanceCNV’s: less than 1% of casesDe novo mutations: 10-20% of cases
valproic acid, rubella, infections during pregnancy, alcohol, thalidomide, parental age, antidepressants, something else?
aberrant functional connectivity and structure not reproducible
biased and unreliable“gold standard”
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Research in Progress1. Brain structure2. Behavioral Phenotype3. Genetic Signature of Behavior
1. Meta analysis of Brain Function2. Gene Expression3. Evaluation
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Why is this work meaningful?
A new model of neuropsychiatric disorder based on patterns of local brain structure
neuropsychiatric profile
brain phenotyp
e
cognitive phenotyp
e
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1. Brain Structure to Predict ASD
• N=400 samples• M=276 features
– Area– Volume – Curvature– Thickness
brain phenotyp
e
cognitive phenotyp
e
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2. Behavioral Phenotype
“Eye gaze score”
What is the developmental trajectory of eye gaze?
0: normal 1: aberrant
• National Database of Autism Research (NDAR)• ~150-200 behavioral metrics• “eye”,“gaze”: 678 questions for 22,823
subjects
cognitive phenotyp
e
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2. Behavioral PhenotypeASD vs. Healthy Control Eye Gaze Scores
Two Sample T-Testt = 46.315, p-value < 2.2e-16
score
Freq
uenc
y
N=22,823
autismcontrol
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2. Behavioral PhenotypeEye Gaze Scores by Age
age
scor
e
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2. Behavioral Phenotype
cognitive phenotyp
e
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3. Genetic Signature of Behavior
Social deficitsCommunication deficitsRepetitive behaviors
ASD
Brain Map
Meta Analysis of Brain Function
“anxiety” 525 Terms
http://vbmis.com/bmi/project/neuromap/
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GeneExpression
3. Genetic Signature of BehaviorGene Expression
Social deficitsCommunication deficitsRepetitive behaviors
ASD
Brain Map
“anxiety”
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Why is this work meaningful?
GeneExpression
Social deficitsCommunication deficitsRepetitive behaviors
Brain MapBehavior• Clinical solutions:– Autism has no drugs– Identify genetic markers that can be detected
in blood• Genetic signature of a behavior
– Leads us closer to drug solution– Signature indicates likelihood of drug working
for specific kind of ASD
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Mapping behavior to genesGene
ExpressionSocial deficitsCommunication deficitsRepetitive behaviors
Brain MapBehavior
“anxiety”
Neurosynth AllenOverlap
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3. Genetic Signature of BehaviorMatch points in “anxiety” map to Allen Brain Atlas
Neurosynth Allen
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3. Genetic Signature of BehaviorHow to find interesting genes for a behavioral map?
Sample 1Sample 2..Sample N
“anxiety”
0 0 0 0 0 0 1 00 1 0 0 0 0 0 11 0 1 0 0 0 0 00 0 0 0 0 0 0 11 0 0 0 1 0 1 00 0 0 0 0 1 0 10 0 1 0 1 0 0 1
genes0.25 .012 1.201.50 0.80 3.400.80 0.90 1.000.40 .075 0.201.40 0.32 4.500.89 0.21 2.400.70 0.10 1.20
genes
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3. Genetic Signature of BehaviorHow to find interesting genes for a behavioral map?
“anxiety”
0 0 0 0 0 0 1 00 1 0 0 0 0 0 11 0 1 0 0 0 0 00 0 0 0 0 0 0 11 0 0 0 1 0 1 00 0 0 0 0 1 0 10 0 1 0 1 0 0 1
Sam
ples
Gene Probes (~60K)
2 1 2 0 2 1 2 4
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3. Genetic Signature of BehaviorHow to find interesting genes for a behavioral map?
“anxiety”
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• Assess the “relative importance” of each gene probe to define a term
• If predictors in regression are uncorrelated, assessing relative importance means:
3. Genetic Signature of BehaviorHow to find interesting genes for a behavioral map?
Shapley Value Regression
Bigger change = more “important”
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3. Genetic Signature of BehaviorHow to find interesting genes for a behavioral map?
Shapley Value Regression• Assess the “relative importance” of each gene
probe to define a term• If predictors in regression are uncorrelated,
assessing relative importance means:
R2
% variance accounted for by modelquality of model predictors
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3. Genetic Signature of BehaviorHow to find interesting genes for a behavioral map?
Shapley Value Regression• creates a score for each player in a game that
represents that player’s contribution to the total value of the game
Attributes (genes): playersTotal Value: quality of model (R2)
R2 with attribute j
R2 withoutattribute j
Shapley valueof gene j
weight based on n total Predictors, k in model
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3. Genetic Signature of BehaviorHow to find interesting genes for a behavioral map?
Shapley Value Regression• creates a score for each player in a game that
represents that player’s contribution to the total value of the game
Attributes (genes): playersTotal Value: quality of model (R2)
marginal contribution to the R2 from adding the attribute to the model last
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0 0 00 1 01 0 10 0 01 0 00 0 00 0 1
3. Genetic Signature of BehaviorHow to find interesting genes for a behavioral map?
Shapley Value Regression• Assess the “relative importance” of each gene to define a term• Define an expression property: consistent pattern of regulation
0.25 0.12 1.201.50 0.80 3.400.80 0.90 1.000.40 0.75 0.201.40 0.32 4.500.89 0.21 2.400.70 0.10 1.20
Prob
es
Samples
1 0 10 0 00 0 00 1 00 0 01 0 10 0 0
Microarray Expression Condition 1 (B1) Condition 2 (B2)
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3. Genetic Signature of BehaviorHow do I evaluate my gene subsets?
• Gene Set Enrichment Analysis– determines whether an a priori defined set of
genes shows statistically significant, concordant differences between two phenotypes.
Nextbio gene expression data for ASD vs. HCBroad Institute Drug Gene Expression Database
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3. Genetic Signature of BehaviorHow do I evaluate my subsets?
Gene Set Enrichment Analysis
1. Enrichment Score: the degree to which a set S is overrepresented at the extremes of my list
2. Estimate the significance level of the scores3. Multiple hypothesis testing
Subramanian, et. al, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS 2005 102 (43) 15545-15550; published ahead of print September 30, 2005,doi:10.1073/pnas.0506580102
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3. Genetic Signature of BehaviorHow do I evaluate my gene subsets?
• Nextbio gene expression data for ASD vs. HC
Is actual gene expression data in ASD vs HC:
1. overexpressed for any of my behavioral term sets?2. overexpressed for gene sets found aberrant in ASD?3. overexpressed for any functional pathways (C2)
Analysis in Progress!
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3. Genetic Signature of BehaviorHow do I evaluate my gene subsets?
– Broad Institute Drug Gene Expression Database
– Daily Med (disorders with anxiety): Adjustment Disorders Affective Disorders, Psychotic
Neurocirculatory Asthenia Obsessive-Compulsive Disorder Premenstrual Syndrome Seasonal Affective Disorder Panic Disorder
(drugs): Meprobamate Fluvoxamine Clorazepate Dipotassium Alprazolam Chlormezanone Trazodone Lorazepam Temazepam Amobarbital Pentobarbital Oxazepam Secobarbital Diazepam Hydroxyzine Ritanserin Oxprenolol Medazepam Secobarbital Diazepam Meprobamate Fluvoxamine Clorazepate Dipotassium Pentobarbital Amobarbital Alprazolam Chlormezanone Trazodone Lorazepam Temazepam Hydroxyzine Oxazepam Oxprenolol Medazepam
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3. Genetic Signature of BehaviorHow do I evaluate my gene subsets?
– Broad Institute Connectivity map .CEL Files• Extract Log2 transformed normalized data• 17 cell lines, 22K probes, 5 anxiety medications
Is gene expression data in for cells exposed to drugs:
1. overexpressed for any of my behavioral term sets?2. overexpressed for gene sets found aberrant in ASD?3. overexpressed for any functional pathways (C2)
How to define phenotypes?
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AcknowledgementsAdvisorsDennis WallRuss AltmanDaniel Rubin
ColleaguesRuth O’HaraJoachim HallmayerAntonio Hardan
Admin SupportSusan AptekarJohn DiMarioMary Jeanne & NancySteven Bagley
FundingMicrosoft ResearchSGF and NSF
Wall LabMaude DavidLeticia Diaz BeltranJena DanielsMarlena DudaAlex LancasterJack KosmickiJae Yoon-JungNikhila AlbertByron Hinebaugh
Rubin LabFrancisco GimenezRebecca SawyerTiffany Ting Lu
BMI FamilyDiegoBootsPeytonLindaKatieNatalieBethWinnSarahEmilyJonathanErika and Brian & coLukeSam
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Thank you!
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3. Genetic Signature of BehaviorHow to find interesting genes for a behavioral map?
PACall.csv
Contains a present/absent flag which indicates whether the probe's expression is well above background. It is set to 1 when both of the following conditions are met.
1) The 2-sided t-test p-value is lower than 0.01, (indicating the mean signal of the probe's expression is significantly different from the corresponding background). 2) The difference between the background subtracted signal and the background is significant (> 2.6 * background standard deviation).
• Microarray expression• PA Call
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3. Genetic Signature of BehaviorHow unique are spatial maps?
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1. Brain Structure to Predict ASD
• N=400• M=276
– Area– Volume – Curvature– Thickness
Correctly Classified Instances 316 79.4 % Incorrectly Classified Instances 82 20.6 %
rh_rostralmiddlefrontal_arearh_lateraloccipital_arearh_lateraloccipital_thicknessrh_lingual_thicknesslh_lingual_thicknesslh_inferiortemporal_meancurvlh_frontalpole_meancurvVineland_TOTALADI_TOTAL_BVADOS_TOTAL_AADOS_TOTAL_B
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3. Genetic Signature of BehaviorGene Set Enrichment Analysis
1. Calculate an enrichment score (ES) that reflects the degree to which a set S is overrepresented at the extremes of the entire ranked list L.
2. Estimate the significance level of the ES by permuting the phenotype labels and recomputing the ES for permuted data null distribution calculate P value
3. Multiple hypothesis testing
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3. Genetic Signature of BehaviorGene Set Enrichment Analysis
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Brain Structure
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(Age Specific) Brain Structure to Predict ASD
age 9-18 years 18+ years
Correctly Classified 58 100% Incorrectly Classified 0 0
Correctly Classified 69 100% Incorrectly Classified 0 0
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3. Genetic Signature of BehaviorTerms with >75% overlap
childhood : children japanese : chinese default : chinese taskrelated : chinese frequency : card
tracking : words family : videos default : japanese taskrelated : japanese taskrelated : default
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2. Behavioral PhenotypeEye Gaze Scores, Colored by Severity