Novel Linkage Peaks Discovered for Diabetic Nephropathy in Individuals With Type 1 Diabetes

Abstract

Genome-wide association studies (GWAS) and linkage studies have had limited success in identifying genome-wide significantly linked regions or risk loci for diabetic nephropathy (DN) in individuals with type 1 diabetes (T1D). As GWAS cohorts have grown, they have also included more documented and undocumented familial relationships. Here we computationally inferred and manually curated pedigrees in a study cohort of >6,000 individuals with T1D and their relatives without diabetes. We performed a linkage study for 177 pedigrees consisting of 452 individuals with T1D and their relatives using a genome-wide genotyping array with >300,000 single nucleotide polymorphisms and PSEUDOMARKER software. Analysis resulted in genome-wide significant linkage peaks on eight chromosomal regions from five chromosomes (logarithm of odds score >3.3). The highest peak was localized at the HLA region on chromosome 6p, but whether the peak originated from T1D or DN remained ambiguous. Of other significant peaks, the chromosome 4p22 region was localized on top of ARHGAP24, a gene associated with focal segmental glomerulosclerosis, suggesting this gene may play a role in DN as well. Furthermore, rare variants have been associated with DN and chronic kidney disease near the 4q25 peak, localized on top of CCSER1.

Figure 1

Manhattan plot of genome-wide linkage analysis. Plot shows results of genome-wide linkage analysis LOD scores. Analysis showed linkage peaks with genome-wide significant LOD scores >3.3 on chromosomes 2q24.3, 2q37.2, 4q21–22, 4q25, 6p21–22, 20q13.2, and 22q12.1. The highest and widest peak occurs on chromosome 6p HLA region.

Figure 2

Imputed HLA haplotype and genotype frequencies for patients in pedigrees. HLA alleles were imputed using SNP2HLA software and Type 1 Diabetes Genome Consortium reference panel and then combined into HLA haplotypes and genotypes. A: A majority of haplotypes were high T1D risk DRB1*0301-DQA1*0501-DQB1*0201 (DR3) or DR4 haplotypes. B: Moreover, >80% of individuals had either one or two DR4 haplotypes, which further highlights the homogenic genetic risk for T1D in this cohort.

Figure 3

LocusZoom regional association plot of 4q25, showing significant linkage and association signals. The y-axis indicates the −log10 (P values), instead of LOD scores, for both linkage and association results. The purple diamond shows DN linkage P value for the lead SNP in our current linkage study, whereas red circles with rs numbers display association P values from Salem et al. (5). The remaining SNPs are colored according to their r2 correlation with the lead SNP.