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

Authors

Ngan K. Tran
Rodney A. Lea
Samuel Holland
Quan Nguyen
Arti M. Raghubar
Heidi G. Sutherland
Miles C. Benton
Nicholas B. Blackburn, The University of Texas Rio Grande Valley
Joanne E. Curran, The University of Texas Rio Grande Valley
John Blangero, The University of Texas Rio Grande Valley

Document Type

Article

Publication Date

9-30-2021

Abstract

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 (pmin = 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 (pmin = 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.

Comments

© 2021. The Author(s).

Recommended Citation

Tran, N. K., Lea, R. A., Holland, S., Nguyen, Q., Raghubar, A. M., Sutherland, H. G., Benton, M. C., Haupt, L. M., Blackburn, N. B., Curran, J. E., Blangero, J., Mallett, A. J., & Griffiths, L. R. (2021). Multi-phenotype genome-wide association studies of the Norfolk Island isolate implicate pleiotropic loci involved in chronic kidney disease. Scientific reports, 11(1), 19425. https://doi.org/10.1038/s41598-021-98935-4

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Publication Title

Scientific Reports

DOI

10.1038/s41598-021-98935-4

Academic Level

faculty

Mentor/PI Department

Office of Human Genetics