Computational protocol: New insights from GWAS for the cleft palate among han Chinese population

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Protocol publication

[…] - SamplesOur samples consisted of 144 complete case-parent trios with nonsydromic cleft palate only (NSCPO), 59 males, 82 females and 3 unknown gender of the probands. All subjects were self-identified as Western Han Chinese, they were recruited between 2008 and 2013 from the Cleft Surgery Department of West China Hospital of Stomatology, Sichuan University. Written informed consent was obtained from parents on behalf of the children and all affected individuals old enough to give their own consent in this study. The consent procedure and this study approved by the Hospital Ethics Committee (HEC) of West China Hospital of Stomatology, Sichuan University.- GenotypingVenous blood samples were drawn from participants and DNA was extracted by phenol chloroform extraction protocol. The SNP genotyping work was performed using a custom-by-design 2x48-Plex SNPscanTM Kit (Cat#:G0104, Genesky Biotechnologies Inc., Shanghai, China).- Statistical analysis The unaffected parents were underwent Hardy-Weinberg Equilibrium (HWE) analysis and minor allele frequency (MAF) determination. HWE, MAF, allelic TDT and parent-of-origin effects, were calculated using PLINK (). Pairwise LD as both their D’ and r2 were computed for all the SNPs using the haploview program (http://www.broad.mit.edu/haploview/haploview). Genotypic TDT and Likelihood ratio test for epistatic interactions based on genotypic TDTs were determined with R Package trio (v1.4.23) (), all two-way interactions comprised a matrix in genotype format were tested using the function colGxG, without specifying the genes, and the interactions between all 38 (38-1)/2 pairs of the SNPs in a matrix were tested. We used a Bonferonni correction for 38 tests to determine a threshold for formal significance of p=0.0013. […]

Pipeline specifications

Software tools PLINK, Haploview
Application GWAS
Diseases Cleft Lip, Cleft Palate