Multi-phenotype genome-wide association studies of the Norfolk Island isolate implicate pleiotropic loci involved in chronic kidney disease

• Published in: Scientific reports Vol. 11; no. 1; pp. 19425 - 10
• Main Authors: Tran, Ngan K., Lea, Rodney A., Holland, Samuel, Nguyen, Quan, Raghubar, Arti M., Sutherland, Heidi G., Benton, Miles C., Haupt, Larisa M., Blackburn, Nicholas B., Curran, Joanne E., Blangero, John, Mallett, Andrew J., Griffiths, Lyn R.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 30.09.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114; 631/208; 692/4022; 692/699; Adult; Cardiovascular diseases; Creatinine; Diabetes mellitus; Female; Gene frequency; Gene loci; Genetic Loci; Genetic Predisposition to Disease; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genotype & phenotype; Glomerular filtration rate; Humanities and Social Sciences; Humans; Kidney diseases; Kidneys; Male; Melanesia; Middle Aged; multidisciplinary; Phenotype; Phenotypes; Polymorphism, Single Nucleotide; Principal components analysis; Renal Insufficiency, Chronic - epidemiology; Renal Insufficiency, Chronic - genetics; Risk Factors; Science; Science (multidisciplinary); Single-nucleotide polymorphism; Urea; Melanesia; Norfolk Island
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-021-98935-4

Chronic kidney disease (CKD) is a persistent impairment of kidney function. Genome-wide association studies (GWAS) have revealed multiple genetic loci associated with CKD susceptibility but the complete genetic basis is not yet clear. Since CKD shares risk factors with cardiovascular diseases and diabetes, there may be pleiotropic loci at play but may go undetected when using single phenotype GWAS. Here, we used multi-phenotype GWAS in the Norfolk Island isolate (n = 380) to identify new loci associated with CKD. We performed a principal components analysis on different combinations of 29 quantitative traits to extract principal components (PCs) representative of multiple correlated phenotypes. GWAS of a PC derived from glomerular filtration rate, serum creatinine, and serum urea identified a suggestive peak (p min  = 1.67 × 10 –7 ) that mapped to KCNIP4 . Inclusion of other secondary CKD measurements with these three kidney function traits identified the KCNIP4 locus with GWAS significance (p min  = 1.59 × 10 –9 ). Finally, we identified a group of two SNPs with increased minor allele frequencies as potential functional variants. With the use of genetic isolate and the PCA-based multi-phenotype GWAS approach, we have revealed a potential pleotropic effect locus for CKD. Further studies are required to assess functional relevance of this locus.