Research in Progress April 2014

The Genetic Signature of Behavior

Vanessa SochatResearch in Progress

April 1, 2014

Autism Spectrum Disorders (ASD)

• $126 billion annually• ~1% prevalence

Social deficitsCommunication deficitsRepetitive behaviors

ASD

anxiety

PTSD

depression

autism

ADHD

bipolar

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”

Research in Progress1. Brain structure2. Behavioral Phenotype3. Genetic Signature of Behavior

1. Meta analysis of Brain Function2. Gene Expression3. Evaluation

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

1. Brain Structure to Predict ASD

• N=400 samples• M=276 features

– Area– Volume – Curvature– Thickness

brain phenotyp

e

cognitive phenotyp

e

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

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

2. Behavioral PhenotypeEye Gaze Scores by Age

age

scor

e

2. Behavioral Phenotype

cognitive phenotyp

e

3. Genetic Signature of Behavior


ASD

Brain Map

Meta Analysis of Brain Function

“anxiety” 525 Terms

http://vbmis.com/bmi/project/neuromap/

http://vbmis.com/bmi/project/neuromap/

GeneExpression

3. Genetic Signature of BehaviorGene Expression


ASD

Brain Map

“anxiety”

Why is this work meaningful?

GeneExpression


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

Mapping behavior to genesGene

ExpressionSocial deficitsCommunication deficitsRepetitive behaviors

Brain MapBehavior

“anxiety”

Neurosynth AllenOverlap

3. Genetic Signature of BehaviorMatch points in “anxiety” map to Allen Brain Atlas

Neurosynth Allen

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


“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


“anxiety”

• Assess the “relative importance” of each gene probe to define a term

• If predictors in regression are uncorrelated, assessing relative importance means:


Shapley Value Regression

Bigger change = more “important”


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


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


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

0 0 00 1 01 0 10 0 01 0 00 0 00 0 1


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)

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

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


• 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!


– 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


– 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?

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

Thank you!


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

3. Genetic Signature of BehaviorHow unique are spatial maps?

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

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

3. Genetic Signature of BehaviorGene Set Enrichment Analysis

Brain Structure

(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

https://sites.google.com/site/vanessasochat/updates-1/study2incorporationofbrainmorphometryandeyegaze/ADtree_group4.png?attredirects=0

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

2. Behavioral PhenotypeEye Gaze Scores, Colored by Severity

Science

Research in Progress April 2014