Computational protocol: A novel ERAP2 haplotype structure in a Chilean population: implications for ERAP2 protein expression and preeclampsia risk

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Protocol publication

[…] Inter-SNP LD and haplotype block calculations were performed in Haploview using the default parameters for confidence intervals, the four gamete rule and solid spine analysis (Barrett et al. ) (version 4.2). Haplotype structure for the African-American and Chilean populations was determined by genotyping samples for the following five SNPs: rs2549782, rs2548538, rs2248374, rs2287988, and rs1056893. Analysis of 100 paired maternal–fetal samples in the African-American population (n = 200) did not show a haplotype structure differing from what had been previously reported (Andrés et al. ) so no additional samples were tested. Initial analysis of a subset of 100 paired maternal–fetal samples in the Chilean population (n = 200) showed larger variation in linkage between SNPs compared to previously reported populations (Andrés et al. ) so the full set of Chilean fetal samples (n = 1100) was analyzed to clarify the genetic structure. Fetal samples were chosen based on the previously reported fetal SNP association with PE in the African-American population (Hill et al. ). [...] Chi-squared tests implemented in R were used to test for differences in rs2248374, rs2549782 compound genotype counts between Chilean fetal cases and controls. Chi-squared tests implemented in R were used to test for differences in the number of observed versus expected compound genotypes of rs2248374 and rs2549782 in Chilean fetal, maternal, and total samples. Expected genotype counts were based on the observed allele frequencies. For example, the observed frequency of the rs2248374 A allele in Chilean fetal (neonatal) samples was 0.34 and the observed frequency of the rs2548792 T allele was 0.67, resulting in an expected AA,TT frequency of 0.34 × 0.34 × 0.67 × 0.67 = 0.052. A power calculation implemented in R was used to determine our power to detect the AA,TT (rs2248374, rs2549782) compound homozygote in the total Chilean population (fetal + maternal). Fisher's exact tests implemented in Haploview (Barrett et al. ) (version 4.2) were used to test individual SNPs and haplotypes for allelic associations with case–control status and to confirm Hardy–Weinberg equilibrium (HWE). These results were confirmed in the PLINK software package (Purcell et al. ). Chi-squared tests implemented in R were used to test for differences between genotype counts in cases and controls. A Bonferroni corrected P-value was used to account for multiple testing errors. Multiple logistic regression in R and epistasis testing methods implemented in PLINK (Purcell et al. ) were used to determine whether an interaction between rs2549782 and rs2248374 was associated with PE in Chilean fetal samples. […]

Pipeline specifications

Software tools Haploview, PLINK
Application GWAS
Diseases Pre-Eclampsia