Natural variation in four human collagen genes across an ethnically diverse population

Abstract

Collagens are members of one of the most important families of structural proteins in higher organisms. There are 28 types of collagens encoded by 43 genes in humans that fall into several different functional protein classes. Mutations in the major fibrillar collagen genes lead to osteogenesis imperfecta (COL1A1 and COL1A2 encoding the chains of Type I collagen), chondrodysplasias (COL2A1 encoding the chains of Type II collagen), and vascular Ehlers-Danlos syndrome (COL3A1 encoding the chains of Type III collagen). Over the past 2 decades, mutations in these collagen genes have been catalogued, in hopes of understanding the molecular etiology of diseases caused by these mutations, characterizing the genotype-phenotype relationships, and developing robust models predicting the molecular and clinical outcomes. To achieve these goals better, it is necessary to understand the natural patterns of variation in collagen genes in human populations. We screened exons, flanking intronic regions, and conserved noncoding regions for variations in COL1A1, COL1A2, COL2A1, and COL3A1 in 48 individuals from each of four ethnically diverse populations. We identified 459 single-nucleotide polymorphisms (SNPs), more than half of which were novel and not found in public databases. Of the 52 SNPs found in coding regions, 15 caused amino acid substitutions while 37 did not. Although the four collagens have similar gene and protein structures, they have different molecular evolutionary characteristics. For example, COL1A1 appears to have been under substantially stronger negative selection than the rest. Phylogenetic analysis also suggests that the four genes have very different evolutionary histories among the different ethnic groups. Our observations suggest that the study of collagen mutations and their relationships with disease phenotypes should be performed in the context of the genetic background of the subjects.

Figure 1. A visual genotype map of all common alleles (MAF ≥ 0.05) in the four collagen genes

SNPs in each gene were arranged from the 5′ (left) to 3′ (right). Each row represents an individual in one of the four ethnic groups: African American (black), European American (blue), Mexican American (green), and Chinese American (red). Homozygous major alleles are represented in blue, heterozygous loci in green, and homozygous minor alleles in yellow. Within each ethnic group, individuals were further clustered by samples using the VG2 program available from the Nickerson group at SeattleSNP (http://pga.gs.washington.edu/VG2.html).

Figure 2. Phylogenetic trees for the four collagen genes

Genotype data from Figure 1 were used to determine the four-way Reynolds distances and phylogenetic trees were generated using the PHYLIP software package.