Editors: Donna E. Hansel, MD, PhD, division head of pathology and laboratory medicine, MD Anderson Cancer Center, Houston; James Solomon, MD, PhD, assistant professor, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York; Erica Reinig, MD, assistant professor and medical director of molecular diagnostics, University of Wisconsin-Madison; Marcela Riveros Angel, MD, molecular genetic pathology fellow, Department of Pathology, Oregon Health and Science University, Portland; Maedeh Mohebnasab, MD, assistant professor of pathology, University of Pittsburgh; Alicia Dillard, MD, associate clinical laboratory director, Omniseq/Labcorp, Buffalo, NY; and Richard Wong, MD, PhD, assistant professor of pathology, University of California San Diego.
Link between APOL1 variants and chronic kidney disease in West Africans
April 2025—Chronic kidney disease is more common in people of African ancestry, with Americans of African descent having four times the risk compared with Americans of European descent. This disparity is largely due to the G1 and G2 genetic variants in the APOL1 gene, which increase the risk of developing chronic kidney disease (CKD) when inherited in a homozygous or compound heterozygous pattern. These variants, exclusive to African populations, likely evolved over 10,000 years ago due to their protective role against African sleeping sickness. The prevalence of these variants varies across sub-Saharan Africa, and data on their connection to CKD in African populations are limited. The authors conducted a study in which they examined West Africans to understand APOL1-related CKD risk. The study involved 8,355 participants, ages one to 74 years, and the study population was 63.3 percent Nigerian and 36.7 percent Ghanaian. The study included 5,578 people with CKD and 2,777 without the disease, with those in the CKD group defined as having CKD stages between two and five or biopsy-confirmed glomerular disease. Study participants with CKD had higher blood pressure and were more likely to have hypertension and diabetes than participants without CKD. The G1 and G2 variants were genotyped, and participants were assessed for zero, one, or two copies of six genotypes based on the presence of risk alleles. The authors used recessive genetic models to compare those with two risk alleles (high risk) to those with one risk allele or no risk alleles (low risk). Forty-three percent of study participants carried one APOL1 risk allele and 29.7 percent carried two. High-risk genotypes were more common in those with CKD (31.6 percent) than in those without the disease (25.7 percent), indicating a dose-response relationship between APOL1 risk alleles and CKD risk. In biopsy-confirmed cases, the most common kidney diseases were minimal change disease, focal segmental glomerulosclerosis, lupus nephritis, and membranous nephropathy. High-risk APOL1 carriers had an 84 percent higher odds of having focal segmental glomerulosclerosis than low-risk carriers, but no significant association was found between APOL1 variants and other kidney diseases. The study suggests that carrying one APOL1 risk allele could predispose a person to CKD, particularly when combined with other genetic or environmental factors. No association was found between APOL1 variants and CKD in study participants with diabetes, suggesting that APOL1 plays a greater role in nondiabetic CKD. The prevalence of APOL1 genotypes varied among different ethnolinguistic groups in West Africa, indicating that ethnicity should be considered in genetic risk assessments for CKD. While the study supports the importance of APOL1 genotyping for CKD risk, it also has limitations, including its focus on CKD patients and a lack of screening for newer APOL1 variants. The authors concluded that the study underscores the significant role of APOL1 in CKD risk, particularly in sub-Saharan Africa, and highlights the need for further research on genetic risk factors in other populations.
Gbadegesin RA, Ulasi I, Ajayi S, et al; H3Africa Kidney Disease Research Network. APOL1 bi- and monoallelic variants and chronic kidney disease in West Africans. N Engl J Med. 2025;392(3):228–238.
Correspondence: Dr. Akinlolu Ojo at aojo@kumc.edu
Validation of a quantitative methylation assay for BRCA1 and RAD51C in breast and ovarian cancers
PARP inhibitors are effective in cancers with mutations in such genes as BRCA1 and BRCA2, which affect the homologous recombination repair pathway. However, some patients who lack these mutations also respond to PARP inhibitors (PARPi), suggesting that defects in homologous recombination repair (HRR) may occur via mechanisms beyond genetic mutation. One such mechanism is epigenetic silencing of BRCA1 and RAD51C via complete promoter hypermethylation, which results in HRR deficiency and increased sensitivity to PARPi. Several studies have explored the association between BRCA1 promoter methylation and PARPi response, but the results were inconsistent, likely due to the limitations of methylation-sensitive polymerase chain-reaction (PCR) methods that lack the sensitivity necessary to differentiate between partial and complete methylation. More recently, the fully quantitative methylation-sensitive droplet digital PCR method demonstrated that all copies of BRCA1 must be methylated to confer sensitivity to PARPi. Similar findings were noted for RAD51C, although RAD51C hypermethylated tumors are less common. The frequency of BRCA1 and RAD51C promoter methylation varies based on tumor type and disease stage. For example, BRCA1 methylation is present in approximately three percent of primary breast cancers but increases to approximately 26 percent in early stage triple-negative breast cancers. Complete epigenetic silencing of the BRCA1 or RAD51C gene (defined as at least 70 percent methylation) is associated with HRR deficiency and sensitivity to PARPi. A major challenge of using promoter methylation to predict response to PARPi is that methylation may be lost during patient treatment, leading to HRR proficiency and, thereby, resistance to PARPi. Monitoring methylation status during therapy, particularly through circulating tumor DNA, could be useful in predicting and addressing resistance to therapy. The authors reported on the development and validation of a BRCA1 and RAD51C methylation (BRM) test that can be run using a one-day library preparation workflow that incorporates bisulfite conversion, making it adaptable to next-generation sequencing (NGS) platforms. The test was used to successfully analyze clinical samples of varying DNA quality, even those with degraded DNA. Methylation-sensitive droplet digital PCR was employed as the gold standard for comparison. The results demonstrated strong correlation between the NGS-based BRM test and droplet digital PCR. The test was able to detect methylation even at DNA input as low as 40 pg and showed high reproducibility, with a linear regression model indicating strong correlation with expected methylation levels. The method also accounted for bisulfite-induced DNA degradation and PCR amplification artifacts, ensuring accurate quantification of methylation. The analytical limit of detection for the BRM test was 2.5 percent methylation based on reference DNA mixtures, and the clinical limit of detection was 10 percent to account for normal tissue contamination in low tumor-content samples. When the test was applied to clinical samples, it identified complete methylation in seven percent of samples, partial methylation in 24 percent, and no methylation in 69 percent, aligning with the findings of previous studies. Methylation patterns can be dynamic, with therapy potentially altering methylation levels, which is why it is critical to monitor patients during treatment. Next-generation sequencing was shown to quantify methylation levels across both promoters, making it a useful tool for identifying patients who may benefit from PARPi therapy. Further research into specific CpG sites within RAD51C and other HRR-related genes could improve predictive accuracy for response to PARPi.
Fink JL, Jaradi B, Stone N, et al. Validation and performance of quantitative BRCA1 and RAD51C promoter hypermethylation testing in breast and ovarian cancers. J Mol Diagn. 2025;27(2):139–153.
Correspondence: Dr. Lynn Fink at lynn.fink@lifestrandsgx.com.au