Copy Number Variation at the APOL1 Locus.
Two coding variants in the APOL1 gene (G1 and G2) explain most of the high rate of kidney disease in African Americans. APOL1-associated kidney disease risk inheritance follows an autosomal recessive pattern: The relative risk of kidney disease associated with inheritance of two high-risk variants is 7-30 fold, depending on the specific kidney phenotype. We wished to determine if the variability in phenotype might in part reflect structural differences in APOL1 gene. We analyzed sequence coverage from 1000 Genomes Project Phase 3 samples as well as exome sequencing data from African American kidney disease cases for copy number variation. 8 samples sequenced in the 1000 Genomes Project showed increased coverage over a ~100kb region that includes APOL2, APOL1 and part of MYH9, suggesting the presence of APOL1 copy number greater than 2. We reasoned that such duplications should be enriched in apparent G1 heterozygotes with kidney disease. Using a PCR-based assay, we observed the presence of this duplication in additional samples from apparent G0G1 or G0G2 individuals. The frequency of this APOL1 duplication was compared among cases (n = 123) and controls (n = 255) with apparent G0G1 heterozygosity. The presence of APOL1 duplication was observed in 4.06% of cases and 0.78% controls, preliminary evidence that this APOL1 duplication may alter susceptibility to kidney disease (p = 0.03). Taqman-based copy number assays confirmed the presence of 3 APOL1 copies in individuals positive for this specific duplication by PCR assay, but also identified a small number of individuals with additional APOL1 copies of presumably different structure. These observations motivate further studies to better assess the contribution of APOL1 copy number on kidney disease risk and on APOL1 function. Investigators and clinicians genotyping APOL1 should also consider whether the particular genotyping platform used is subject to technical errors when more than two copies of APOL1 are present.
Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America; Division of Nephrology, Department of Medicine, University of Florida, Gainesville, Florida, United States of America; Harvard Medical School, Boston, Massachusetts, United States of America.
Rupam
R
Ruchi
Stanley Center, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.
Giulio
G
Genovese
Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America.
Jessica
J
Lee
Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America.
Victoria T
VT
Charoonratana
Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America.
Andrea J
AJ
Bernhardy
Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America; Harvard Medical School, Boston, Massachusetts, United States of America; Stanley Center, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.
Seth L
SL
Alper
Kidney Diseases Branch, National Institutes of Health, Bethesda, Maryland, United States of America.
Jeffrey B
JB
Kopp
Renal Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States of America.
Ravi
R
Thadhani
Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America; Harvard Medical School, Boston, Massachusetts, United States of America; Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America.
David J
DJ
Friedman
Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America; Harvard Medical School, Boston, Massachusetts, United States of America; Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.
Martin R
MR
Pollak
D001741:Black or African American; D000075944:Apolipoprotein L1; D001053:Apolipoproteins / Q000235:genetics*; D000075943:Apolipoproteins L; D016022:Case-Control Studies; D056915:DNA Copy Number Variations; D020440:Gene Duplication; D015870:Gene Expression; D005787:Gene Frequency; D005808:Genes, Recessive; D056426:Genetic Loci; D020022:Genetic Predisposition to Disease; D015894:Genome, Human; D006579:Heterozygote; D016045:Human Genome Project; D006801:Humans; D007668:Kidney / Q000378:metabolism / Q000473:pathology; D007674:Kidney Diseases / Q000175:diagnosis / Q000208:ethnology / Q000235:genetics* / Q000473:pathology; D008075:Lipoproteins, HDL / Q000235:genetics*; D020409:Molecular Motor Proteins / Q000235:genetics; D018995:Myosin Heavy Chains / Q000235:genetics; D010375:Pedigree; D012306:Risk
C108666:APOL1 protein, human; C543112:APOL2 protein, human; D000075944:Apolipoprotein L1; D001053:Apolipoproteins; D000075943:Apolipoproteins L; D008075:Lipoproteins, HDL; C103814:MYH9 protein, human; D020409:Molecular Motor Proteins; D018995:Myosin Heavy Chains