Computational protocol: Association study of stuttering candidate genes GNPTAB, GNPTG and NAGPA with dyslexia in Chinese population

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Protocol publication

[…] In total, 21 Tag SNPs covering GNPTAB, GNPTG and NAGPA were selected through Tagger program [] with parameters of minor allele frequency (MAF) over 5% and pairwise r2 threshold of 0.8. The SNP genotyping was performed on SequenomMassARRAY platform (Sequenom, San Diego, CA) at CapitalBio Corporation (Beijing, China). Genomic DNA samples were extracted from saliva samples using Oragene™ DNA self-collection kit (DNA Genotek Inc., Ottawa, Ontario, Canada) and DNA quantity was determined by Nanodrop spectrophotometry (Nanodrop 1000 Spectrophotometer, Thermo Scientific, Wilmington, DE). A locus-specific PCR reaction based on a locus-specific primer extension reaction was designed using the MassARRAY Assay Design software package (v3.1). MALDI-TOF mass spectrometer and Mass ARRAY Type 4.0 software were used for mass determination and data acquisition. [...] Statistical analysis was undertaken using PLINK software (http://pngu.mgh.harvard.edu/~purcell/plink/), which is an open-source whole genome association analysis toolset and is commonly used to perform a range of basic, large-scale analyses []. Hardy-Weinberg equilibrium (HWE) tests were undertaken for each SNP, and association tests were performed using additive, dominant, or recessive genetic models. Haplotype analyses were performed using Haploview software (Version 4.2). Haploview is a software package that provides computation of linkage disequilibrium (LD) in genetic data, performs association studies, chooses tagSNPs and estimates haplotype frequencies [,]. Chi square tests were used to test for haplotype association and full model association (Genotype, Dom, Rec). A Fisher’s exact test was used for allelic association. Logistic regression was applied for risk stratification with or without covariate (age and sex) in both single marker and haplotype analysis. False discovery rate (FDR) correction for multiple testing was undertaken for the 21 SNPs that were adopted into the single site association analysis. […]

Pipeline specifications

Software tools Tagger, PLINK, Haploview
Application GWAS
Organisms Homo sapiens