Mutations in Collagen Genes in the Context of an Isolated Population

Abstract

Genetic studies of population isolates have great potential to provide a unique insight into genetic differentiation and phenotypic expressions. Galičnik village is a population isolate located in the northwest region of the Republic of North Macedonia, established around the 10th century. Alport syndrome-linked nephropathy with a complex inheritance pattern has been described historically among individuals in the village. In order to determine the genetic basis of the nephropathies and to characterize the genetic structure of the population, 23 samples were genotyped using a custom-made next generation sequencing panel and 111 samples using population genetic markers. We compared the newly obtained population data with fifteen European population data sets. NGS analysis revealed four different mutations in three different collagen genes in twelve individuals within the Galičnik population. The genetic isolation and small effective population size of Galičnik village have resulted in a high level of genomic homogeneity, with domination of R1a-M458 and R1b-U106* haplogroups. The study explains complex autosomal in cis digenic and X-linked inheritance patterns of nephropathy in the isolated population of Galičnik and describes the first case of Alport syndrome family with three different collagen gene mutations.

Keywords: Alport syndrome; Galičnik; benign familial hematuria; digenic inheritance; isolated population.

Figure 1

Geographic location of Galičnik village in the Republic of North Macedonia. The map was modified from https://en.wikipedia.org/wiki/Statistical_Regions_of_Macedonia.

Figure 2

Pedigree tree of the Galičnik family having digenic autosomal inheritance with mutation in COL4A3 and COL4A4 in cis and X-linked COL4A5 mutation.

Figure 3

Population structure of the Galičnik samples. Left: Principal component analysis (PCA) of the Galičnik samples with 14 European populations based on raw haplogroups frequencies. Right: Multidimensional scaling (MDS) analysis of the Galičnik samples with 15 European populations based on Rst distance matrix of YSTR haplotypes (AT-Austria, BIH-Bosnia and Herzegovina, BUL-Bulgaria, CRO-Croatia, CZE-Czechia, GAL-Galičnik, HUN-Hungary, ITA-Italia, MK-North Macedonia, MNE-Montenegro, POL-Poland, RUS-Russia, SER-Serbia, SLO-Slovenia, SVK-Slovakia).

Figure 4

Heatmap based on the average number of pairwise differences (Rst) between populations, within populations, and corrected average pairwise difference.

Figure 5

Median-joining network based on 24 Galičnik YSTR haplotypes within the R1a1a (M198) haplogroup. The size of each circle corresponds to the number of individuals belonging to that haplotype. Yellow circles represent haplotypes identified in Galičnik individuals. The lengths of the lines correspond to the number of mutational differences between haplotypes.