Computational protocol: Common Variants in the COL4A4 Gene Confer Susceptibility to Lattice Degeneration of the Retina

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Protocol publication

[…] For MS genotyping, statistical significance of differences was assessed by Fisher’s exact test using the 2×2 and 2×m (where m is the number of alleles) contingency tables for each allele. Allele frequencies in pooled DNA stages were estimated from the height of the peaks; each allele frequency was determined by dividing the height of each allele peak by the summed height of all allele peaks. For the exact probability test, the Markov chain/Monte Carlo simulation method was employed to execute the Fisher’s exact test for the 2×m contingency table. The smallest P value for each marker was selected. In the individual MS genotyping stage, the probability of association was corrected by the Bonferroni’s method, i.e. by multiplying the obtained P values with the number of observed alleles at the locus (corrected P [Pc] value). Association analyses for the SNP genotyping stage were carried out using Haploview 4.1 and obtained P values were corrected for multiple testing by a permutation test (10,000 iterations) using Haploview. Haploview 4.1 was also used to compute pairwise LD statistics. Haplotype frequencies in the multi-locus analyses were calculated using PyPop 0.7.0 . Haplotype frequencies were estimated using the iterative Expectation-Maximization algorithm. LD was measured using Hedrick’s multiallelic D’ statistic . Differences in COL4A4 mRNA expression levels were analyzed via the Mann-Whitney U test. […]

Pipeline specifications

Software tools Haploview, PyPop
Applications Population genetic analysis, GWAS
Organisms Homo sapiens
Diseases Retinal Detachment, Retinal Diseases