Fig. 3: Genetic features of structural variation and gene conversion in IGKV. | Genes & Immunity

Fig. 3: Genetic features of structural variation and gene conversion in IGKV.

From: Resolving haplotype variation and complex genetic architecture in the human immunoglobulin kappa chain locus in individuals of diverse ancestry

Fig. 3

A Diagram of structural polymorphisms in the IGK locus, including a gene conversion event in which ~16 Kbp of sequence containing IGKV1-12 and IGKV1-13 replaced paralogous sequence in the distal region, described previously [14]. Also shown is an inversion spanning the proximal and distal regions from IGKV1-27 to IGKV1D-27 with a length of ~ 1.301 Mbp (see Fig. S12), and a 24.7 Kbp deletion SV that includes the gene IGKV1-NL1. B Stacked bar plot indicating the SV genotype frequencies for each population, with “1” corresponding to deletion. C Stacked bar plot indicating the gene conversion haplotype frequency for each population, with “1” corresponding to the conversion haplotype. D Boxplot of the SNV density difference between distal and proximal regions with samples grouped according to their genotype for the gene conversion (left) as well as population (right). SNV densities were computed for 10 Kbp windows along the proximal and distal regions from alignments of IGK proximal assemblies to the proximal region of our custom reference and, likewise, alignments of IGK distal assemblies to the distal region of our custom reference (see Materials and Methods). For each sample, the mean SNV density for the distal region was subtracted from the mean SNV density value for the proximal region. E (Top) SNV densities in 10 Kbp windows along the IGK distal region (chr2:89859172-90266726). IGKV genes in this interval are labeled along the x-axis. Each line represents a sample. Samples are grouped according to their genotype for the gene conversion. (Bottom) Genotypes (colors) at each variant position for the corresponding coordinates above. The “.” symbol represents deletion. Hierarchical clustering of samples (rows) resulted in the 3 indicated clusters. F Principal component analysis of samples based on SNVs (MAF ≥ 2.86%) in the IGK distal region. Samples are colored by population (left) or gene conversion genotype (right). EV1: eigenvector 1, EV2: eigenvector 2.

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