evidence of gene-environment interaction for the runx2 gene

8/2/2019 Evidence of Gene-Environment Interaction for the RUNX2 Gene

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Evidence of gene-

environment interactionfor the RUNX2 gene andEnvironmental tobaccosmoke in controlling therisk of cleft lip

with/without cleftpalate


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The paper

Examined 49 markers in the Runt-relatedtranscription factor 2 (RUNX2) gene andnonsyndromic cleft lip with/without cleft palate

326 Chinese case-parent trios

Looked at GxE interactions and parent of origineffects

5 SNPs showed significant evidence of linkage inassociation with CL/P

Compelling evidence between markers inRUNXC2 and ETS (environmental tobaccosmoke)


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Background RUNX2Gene located on chromosome 6p21

Encode for a TF critical for osteoblasticdifferentiation

Thought to be under oestrogen control for

osteoblast- and osteoclasto-gensisMutations of RUNX2 in humans lead to

cleidocranial dysplasia (heritable)

Missing clavicles dental abnormalities and

craniofacial abnormalities, can include clefting

Animal models suggests mutations andexpression levels of RUNX2 maybe involved inthe development of several craniofacial defects

Has genotypes for association with CL/P but


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Approach takenTrios recruited in 3 sites mainly in China

None of the parents had the disorder

Collected a lot of data but only looked at ETS andmultivitamin supplementation because the numbers formaternal cigarette smoking and alcohol consumptionwere so low (only 1%)

High rate of Chinese men smoke = exposure

An association analyses of case-parent trios from fourpopulations also suggested RUNX2 may influence risk ofCL/P through imprinting effects

69 selected SNPs were selected from designed coresprovided by illumina, 20 monomorphic ones dismissed.No mendelian inconsistencies found in minor allelefrequencies from the remainder polymorphic 49 andranged from 5% to 47.6%


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ApproachPairwise linkage disequilibrium (LD) was measured as r2 for

all SNPs using the Haploview program, and was used toidentify LD blocks

To assess the significance of TDT (TransmissionDisequilibrium Test) findings while considering multiple tests,the permutation test in PLINK was used to get corrected pvalues

The family association test program (FBAT) was used forhaplotype anaylsis

Sliding window approach for haplotypes to systematicallyanalyze all adjacent 2-SNP and 3-SNP combinations

Plots of log10 (p value) for individual SNPs and haplotypeswere generated using the R package snp.plotter

Conditional logistic regression under additive models toestimate the relative risk (RR) for being a case with orwithout environmental exposures for each SNP

Tested for log-additive GxE interaction


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Approach

Estimated haplotype-environment interaction wherefamily-based association tests are evaluated whileallowing for a potential GxE interaction in a 2 degreeof freedom (df) test, followed by a separate 1 df testfor GxE interaction alone

The 2 df test examines the genetic effect of ahaplotype while taking into account possible effects ofGxE interaction, while the 1 df test investigates theeffect of GxE interaction alone

Parent-of-origin effects were also tested using severalmethods

transmission asymmetry test (TAT) used to checkfor potential parent-of-origin effects, A significantTAT could reflect an imprinting effect or a maternal

genotype effect- - -


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Replication study

In silico replication study usingsamples from European and Asianancestry from a GWAS ofnonsyndromic CL/P using a case-parent design by another study

78 SNPs in RUNX2 were genotypedand analysed similarly

TDT analysis in PLINK, tested GxEinteraction using conditional logisticregression models, PBAT to confirm findingsseen in Chinese trios


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Results

9 independentSNPs and 8blocks oflinkage

disequilibriumwere identified


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Results 5 SNPs in the RUNX2 gene showed significant linkage in

the presence of associations with nonsyndromic CL/P.One of these remained significant after in permutationtests.

These findings were replicated in 825

European case parent trios.


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ResultsSingle SNP analysis using conditional logistic

regression models and haplotype analysisusing PBAT suggested the RUNX2 gene mayalso influence the risk of CL/P throughinteraction with ETS and multivitamin

supplementation. Independent samples from European populations

showed consistent evidence of significant GxETSinteraction at two SNPs.

One SNP showed marginally significantmaternal over-transmission after consideringmaternal genotypic effects


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Criticism

Average sample size


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Criticism

Very poorly defined criteria for ETS

Did not specify what multivitaminsupplementation was (Contained folic acid?Dose?)

Didnt look at null effects of having genotypebut no phenotype (are there any kids with thegenotype but no phenotype?)

Low diversity in sample population, couldhave incorporated other ethnicities

Only looked at one gene for interaction withETS/ multivitamin supplementation


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Other environmentalfactorsGeneral pollution / radiation exposure

Alcohol intake

Binge drinking?

Diet and food hygiene

Other physiological diseases/ disordercarried by the parents

Stress

Awareness and precautions forplanned pregnancies


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Other genes in thepathway


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Other genes in thepathway


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Other genes

Other studies have investigatedcommon environmental factors(eg. smoking, alcohol,

multivitamin/ folic acidsupplementation, midication)with allele variants in other genes

TGFA, TGB3, MSX1, BCL3, RARA,MTHFR, CYP1A1, MAT1, MAT2,GSTT1, EPHX1


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GxE GWAS approach

Possible given the new wave ofsequencing approaches andcomputational advances

Many caveats will be problematic Large sample size with systematic accuracy

Easier with a disease/disorder with a singular,easily characterized phenotype

Well defined parameters

evidence of gene-environment interaction for the runx2 gene

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