The Effect of Inversion at 8p23 on <i>BLK</i> Association with Lupus in Caucasian Population

<div><p>To explore the potential influence of the polymorphic 8p23.1 inversion on known autoimmune susceptibility risk at or near <i>BLK</i> locus, we validated a new bioinformatics method that utilizes SNP data to enable accurate, high-throughput genotyping of the 8p23.1 inversion in a Caucasian population. Methods: Principal components analysis (PCA) was performed using markers inside the inversion territory followed by k-means cluster analyses on 7416 European derived and 267 HapMaP CEU and TSI samples. A logistic regression conditional analysis was performed. Results: Three subgroups have been identified; inversion homozygous, heterozygous and non-inversion homozygous. The status of inversion was further validated using HapMap samples that had previously undergone Fluorescence in situ hybridization (FISH) assays with a concordance rate of above 98%. Conditional analyses based on the status of inversion were performed. We found that overall association signals in the <i>BLK</i> region remain significant after controlling for inversion status. The proportion of lupus cases and controls (cases/controls) in each subgroup was determined to be 0.97 for the inverted homozygous group (1067 cases and 1095 controls), 1.12 for the inverted heterozygous group (1935 cases 1717 controls) and 1.36 for non-inverted subgroups (924 cases and 678 controls). After calculating the linkage disequilibrium between inversion status and lupus risk haplotype we found that the lupus risk haplotype tends to reside on non-inversion background. As a result, a new association effect between non-inversion status and lupus phenotype has been identified ((p = 8.18×10⁻⁷, OR = 1.18, 95%CI = 1.10–1.26). Conclusion: Our results demonstrate that both known lupus risk haplotype and inversion status act additively in the pathogenesis of lupus. Since inversion regulates expression of many genes in its territory, altered expression of other genes might also be involved in the development of lupus.</p></div

Association and comparisons of minor allele frequency of known SNP rs13277113 for lupus according to three identified Caucasian subgroups.

<p>Association and comparisons of minor allele frequency of known SNP rs13277113 for lupus according to three identified Caucasian subgroups.</p

Demographic distribution of the individuals in the study^*.

<p>* Values are the number of patients/number of controls.</p><p>Demographic distribution of the individuals in the study^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0115614#nt101" target="_blank">*</a>}.</p

PCA analyses on 7683 Caucasian derived samples and identification of three subgroups at 8p23.

<p>Group 1 =  Inverted-homozygous, Group 2 =  Heterozygous, Group 3 =  Non-inverted homozygous.</p

The logistic regression conditional analyses and association results of selected top markers known to be associated with lupus.

<p>*R2: correlation coefficient as a measure of linkage disequilibrium between inversion status and reported marker in Caucasian population.</p><p>**P-original =  the original case control association results adjusted for three ordinary principal components.</p>†<p>Inversion as a genotype call. N = Non-inversion, I =  Inversion</p><p>The logistic regression conditional analyses and association results of selected top markers known to be associated with lupus.</p

Comparisons of minor allele frequency differences of a known published SNP associated with lupus (rs13277113) in 3 different Caucasian subgroups.

<p>Comparisons of minor allele frequency differences of a known published SNP associated with lupus (rs13277113) in 3 different Caucasian subgroups.</p

A schematic representation of the association map for Lupus at 8p23 before and after conditional analyses.

<p>Red dots =  original association, Blue dots = Association effects after conditioning on inversion. R2 =  correlation coefficient as a measure of linkage disequilibrium between inversion status and all markers in Caucasian population. The highest region in LD with inversion is shown with vertical line at LINC00208.</p

Cluster analyses using K-means clustering with squared Euclidean distance measurement.

<p>PC value is a numerical value obtained from STRUCTURE PC1 vector for each individual. In this approach the algorithm attempts to find the centers of the clusters in order to minimize the sum of the distances within each cluster.</p

A schematic representation of haplotype block of 3 published lupus related snps at or near BLK and their degree of LD (r2) with inversion status (rs2736340, rs13277113, rs2618476). INVER = putative inversion variant.

<p>A schematic representation of haplotype block of 3 published lupus related snps at or near BLK and their degree of LD (r2) with inversion status (rs2736340, rs13277113, rs2618476). INVER = putative inversion variant.</p

The haplotype frequencies of the three known SNPs (rs2736340, rs13277113, rs2618476) and their relation with inversion status.

<p>I = Inverted, N = Non-inverted.</p><p>The non-inverted status is in LD with the known risk haplotype AAG (italics).</p><p>The haplotype frequencies of the three known SNPs (rs2736340, rs13277113, rs2618476) and their relation with inversion status.</p