Computational protocol: CNTNAP2 variants affect early language development in the general population

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Protocol publication

[…] Our panel of 30 SNPs matching those used to study SLI in previous CNTNAP2 analyses () constituted the majority of the 38 SNPs assessed in the prior study. Each biallelic SNP was first tested for association with the quantitative measure of the communication phenotype using an allelic test of association within R (). On the basis of the previous findings by , our model assumed that the risk allele of the SNP had a dominant mode of action. Consideration of the singlepoint SNP findings, and their convergence with earlier studies, led us to test the four-marker haplotypes of rs2710102–rs759178–rs17236239–rs2538976, analyzing the three common alleles using R. Our analysis of each such multimarker allele involved two factors: (1) comparison between harboring two copies and one copy of the haplotype and (2) comparison between harboring two copies and no copies of the haplotype – allowing us to separately assess the modes of action of each of the three alleles. To minimize multiple testing, we did not analyze any further marker configurations. Linkage disequilibrium (LD) among CNTNAP2 SNPs was determined with Haploview version 4.2 (http://www.broadinstitute.org/haploview/haploview) (). Haplotypes were inferred using SimHap version 1.0.2, and the most-likely haplotypes of each individual used as inputs for the R analyses described above.Principal components analysis of genome-wide SNP data with Eigenstrat () has revealed evidence of population stratification in the Raine sample, and so the first two principal components were included as cofactors in all analyses. This procedure has been used previously in genetic analyses of the Raine cohort (). […]

Pipeline specifications

Software tools Haploview, SimHap
Application GWAS
Organisms Homo sapiens
Diseases Congenital, Hereditary, and Neonatal Diseases and Abnormalities