Analytical Validation of a Personalized Medicine APOL1 Genotyping Assay for Nondiabetic Chronic Kidney Disease Risk Assessment

Abstract

The incidence of chronic kidney disease (CKD) varies by ancestry, with African Americans (AA) having a threefold to fourfold higher rate than whites. Notably, two APOL1 alleles, termed G1 [c.(1072A>G; 1200T>G)] and G2 (c.1212_1217del6), are strongly associated with higher rates of nondiabetic CKD and an increased risk for hypertensive end-stage renal disease. This has prompted the opportunity to implement APOL1 testing to identify at-risk patients and modify other risk factors to reduce the progression of CKD to end-stage renal disease. We developed an APOL1 genotyping assay using multiplex allele-specific primer extension, and validated using 58 positive and negative controls. Genotyping results were completely concordant with Sanger sequencing, and both triplicate interrun and intrarun genotyping results were completely concordant. Multiethnic APOL1 allele frequencies were also determined by genotyping 7059 AA, Hispanic, and Asian individuals from the New York City metropolitan area. The AA, Hispanic, and Asian APOL1 G1 and G2 allele frequencies were 0.22 and 0.13, 0.037 and 0.025, and 0.013 and 0.004, respectively. Notably, approximately 14% of the AA population carried two risk alleles and are at increased risk for CKD, compared with <1% of the Hispanic and Asian populations. This novel APOL1 genotyping assay is robust and highly accurate, and represents one of the first personalized medicine clinical genetic tests for disease risk prediction. (J Mol Diagn 2016, 18: 260e266; http://dx.doi.org/10.1016/j.jmoldx.2015 Chronic kidney disease (CKD) is a progressive loss of renal function that can be defined by laboratory findings, such as pathological abnormalities, composition of blood or urine, and decreased glomerular filtration rates. 1 CKD is classified into five different stages according to the presence or absence of kidney damage and the level of kidney function, and its symptoms include hypertension, anemia, hyperkalemia, metabolic acidosis, and bone disease.

APOL1 renal risk variants are associated with obesity and body composition in African ancestry adults

“…We genotyped Bio Me and GUARDD cohorts using a clinical genetic test to determine APOL1 ancestral (G0), G1, and G2 variant status, [ 26 , 31 ] BioVU and NUgene cohorts using a standard genotyping array (with imputation of APOL1 variant status), and the JHS cohort by exome sequencing. [ 32 ]…”

HLA-DQA1 and APOL1 as Risk Loci for Childhood-Onset Steroid-Sensitive and Steroid-Resistant Nephrotic Syndrome

“…The samples were genotyped for the APOL1 G1 and G2 alleles by direct sequencing. Control data was obtained from published figures based on 5,543 African-Americans from the BioMe biobank of the Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York 20 . This is one of the largest samples of African-Americans that were genotyped for the APOL1 G1 and G2 high risk alleles.…”

Plasma biomarkers are associated with renal outcomes in individuals with APOL1 risk variants

“…We genotyped AA Bio Me participants using direct genotyping to determine APOL1 ancestral (G0), G1 and G2 allele status. 31 To validate this genotyping method, we performed intra- and inter- assay variation studies that include 48 positive and 10 negative control samples. Sanger sequencing was used to confirm all of genotypes.…”