A Custom Target Next-Generation Sequencing 70-Gene Panel and Replication Study to Identify Genetic Markers of Diabetic Kidney Disease

Genes (Basel). 2021 Dec 15;12(12):1992. doi: 10.3390/genes12121992.

Abstract

Diabetic kidney disease (DKD) has been pointed out as a prominent cause of chronic and end-stage renal disease (ESRD). There is a genetic predisposition to DKD, although clinically relevant loci are yet to be identified. We utilized a custom target next-generation sequencing 70-gene panel to screen a discovery cohort of 150 controls, DKD and DKD-ESRD patients. Relevant SNPs for the susceptibility and clinical evolution of DKD were replicated in an independent validation cohort of 824 controls and patients. A network analysis aiming to assess the impact of variability along specific pathways was also conducted. Forty-eight SNPs displayed significantly different frequencies in the study groups. Of these, 28 with p-values lower than 0.01 were selected for replication. MYH9 rs710181 was inversely associated with the risk of DKD (OR = 0.52 (0.28-0.97), p = 0.033), whilst SOWAHB rs13140552 and CNDP1 rs4891564 were not carried by cases or controls, respectively (p = 0.044 and 0.023). In addition, the RGMA rs1969589 CC genotype was significantly correlated with lower albumin-to-creatinine ratios in the DKD patients (711.8 ± 113.0 vs. 1375.9 ± 474.1 mg/g for TC/TT; mean difference = 823.5 (84.46-1563.0); p = 0.030). No biological pathway stood out as more significantly affected by genetic variability. Our findings reveal new variants that could be useful as biomarkers of DKD onset and/or evolution.

Keywords: chronic kidney disease; diabetes kidney disease; single nucleotide polymorphisms.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aged
  • Cohort Studies
  • Diabetic Nephropathies / diagnosis
  • Diabetic Nephropathies / genetics*
  • Dipeptidases / genetics
  • Female
  • Gene Expression / genetics
  • Gene Expression Profiling / methods
  • Genetic Markers / genetics
  • Genetic Predisposition to Disease
  • Genotype
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Male
  • Myosin Heavy Chains / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Spain
  • Transcriptome / genetics*

Substances

  • Genetic Markers
  • MYH9 protein, human
  • CNDP1 protein, human
  • Dipeptidases
  • Myosin Heavy Chains