Cases in Precision Medicine: APOL1 and Genetic Testing in the Evaluation of Chronic Kidney Disease and Potential Transplant

Polygenic scores and their applications in kidney disease

Genome-wide association studies (GWAS) have uncovered thousands of risk variants that individually have small effects on the risk of human diseases, including chronic kidney disease, type 2 diabetes, heart diseases and inflammatory disorders, but cumulatively explain a substantial fraction of disease risk, underscoring the complexity and pervasive polygenicity of common disorders. This complexity poses unique challenges to the clinical translation of GWAS findings. Polygenic scores combine small effects of individual GWAS risk variants across the genome to improve personalized risk prediction. Several polygenic scores have now been developed that exhibit sufficiently large effects to be considered clinically actionable. However, their clinical use is limited by their partial transferability across ancestries and a lack of validated models that combine polygenic, monogenic, family history and clinical risk factors. Moreover, prospective studies are still needed to demonstrate the clinical utility and cost-effectiveness of polygenic scores in clinical practice. Here, we discuss evolving methods for developing polygenic scores, best practices for validating and reporting their performance, and the study designs that will empower their clinical implementation. We specifically focus on the polygenic scores relevant to nephrology and other chronic, complex diseases and review their key limitations, necessary refinements and potential clinical applications.

Advancing Genetic Testing in Kidney Diseases: Report From a National Kidney Foundation Working Group

About 37 million people in the United States have chronic kidney disease, a disease that encompasses diseases of multiple causes. About 10% or more of kidney diseases in adults and about 70% of selected chronic kidney diseases in children are expected to be explained by genetic causes. Despite the advances in genetic testing and an increasing understanding of the genetic bases of certain kidney diseases, genetic testing in nephrology lags behind other medical fields. More understanding of the benefits and logistics of genetic testing is needed to advance the implementation of genetic testing in chronic kidney diseases. Accordingly, the National Kidney Foundation convened a Working Group of experts with diverse expertise in genetics, nephrology, and allied fields to develop recommendations for genetic testing for monogenic disorders and to identify genetic risk factors for oligogenic and polygenic causes of kidney diseases. Algorithms for clinical decision making on genetic testing and a road map for advancing genetic testing in kidney diseases were generated. An important aspect of this initiative was the use of a modified Delphi process to reach group consensus on the recommendations. The recommendations and resources described herein provide support to nephrologists and allied health professionals to advance the use of genetic testing for diagnosis and screening of kidney diseases.

Comparison of METS-IR and HOMA-IR for predicting new-onset CKD in middle-aged and older adults

BACKGROUND

Chronic kidney disease (CKD) has emerged as a mounting public health issue worldwide; therefore, prompt identification and prevention are imperative in mitigating CKD-associated complications and mortality rate. We aimed to compare the predictive powers of the homeostatic model assessment for insulin resistance (HOMA-IR) and the metabolic score for insulin resistance (METS-IR) for CKD incidence in middle-aged and older adults.

METHODS

This study used longitudinal prospective cohort data from the Korean Genome and Epidemiology Study. A total of 10,030 participants, aged 40-69 years, residing in the Ansung or Ansan regions of the Republic of Korea, were recruited between 2001 and 2002 through a two-stage cluster sampling method. We compared the predictive powers of METS-IR and HOMA-IR for CKD prevalence and incidence, respectively. CKD prevalence was measured by the area under the receiver operating characteristic (ROC) curve (AUC), and the indices' predictive performance for CKD incidence were assessed using Harrell's concordance index and time-dependent ROC curve analysis.

RESULTS

A total of 9261 adults aged 40-69 years at baseline and 8243 adults without CKD were included in this study. The AUCs and 95% confidence intervals (CIs) of HOMA-IR and METS-IR for CKD prevalence at baseline were 0.577 (0.537-0.618) and 0.599 (0.560-0.637), respectively, with no significant difference (p = 0.337). The Heagerty's integrated AUC for METS-IR in predicting CKD incidence was 0.772 (95% CI 0.750-0.799), which was significantly higher than that of HOMA-IR (0.767 [95% CI 0.742-0.791], p = 0.015).

CONCLUSION

METS-IR surpassed HOMA-IR in predicting CKD incidence and was as effective as HOMA-IR in predicting CKD prevalence. This implies that METS-IR could be a valuable indicator for early detection and prevention of CKD among Korean adults.

Association between the triglyceride–glucose index and chronic kidney disease in adults

BACKGROUND

Chronic kidney disease (CKD) is characterized as a progressive dysfunction of the kidney, and it might have a close relationship with insulin resistance. We utilized the triglyceride-glucose (TyG) index, a reliable marker of insulin resistance, to evaluate the association between the TyG index and CKD in adults from the general population.

METHODS

This was a cross-sectional study obtaining data from the 2015-2018 National Health and Nutrition Examination Survey. The estimated glomerular filtration rate (eGFR) and urinary albumin-to-creatinine ratio (UACR) served as kidney function indicators. We defined CKD as the existence of either low eGFR (eGFR < 60 mL/min/1.73 m² BSA) or albuminuria (UACR > 30 mg/g). Multivariate regressions, correlated subgroup analyses, and interaction terms were performed in this study.

RESULTS

For 4361 recruited participants, the mean TyG index was 8.60 ± 0.68, and the prevalence of CKD was 13.35%. Participants with a higher TyG index showed a higher UACR level (β = 25.10, 95% CI: 6.76, 43.44, P = 0.0074) and higher levels of CKD (OR = 1.34, 95% CI: 1.13, 1.59, P = 0.0006). The positive relationship between the TyG index and CKD became stronger and remained significant in the overweight (OR = 1.61, 95% CI: 1.18, 2.20, P = 0.0027) and obese (OR = 2.48, 95% CI: 1.95, 3.15, P < 0.0001) groups and in people with diabetes (OR = 1.94, 95% CI: 1.46, 2.56, P < 0.0001).

CONCLUSIONS

Higher TyG index was strongly associated with a higher UACR level and higher values of albuminuria and CKD, which might be useful in kidney function screening especially among people in disadvantageous socioeconomic conditions with no availability for direct measurement of kidney function. However, more well-designed studies are still needed to validate this relationship.

Genome-wide polygenic score to predict chronic kidney disease across ancestries

Chronic kidney disease (CKD) is a common complex condition associated with high morbidity and mortality. Polygenic prediction could enhance CKD screening and prevention; however, this approach has not been optimized for ancestrally diverse populations. By combining APOL1 risk genotypes with genome-wide association studies (GWAS) of kidney function, we designed, optimized and validated a genome-wide polygenic score (GPS) for CKD. The new GPS was tested in 15 independent cohorts, including 3 cohorts of European ancestry (n = 97,050), 6 cohorts of African ancestry (n = 14,544), 4 cohorts of Asian ancestry (n = 8,625) and 2 admixed Latinx cohorts (n = 3,625). We demonstrated score transferability with reproducible performance across all tested cohorts. The top 2% of the GPS was associated with nearly threefold increased risk of CKD across ancestries. In African ancestry cohorts, the APOL1 risk genotype and polygenic component of the GPS had additive effects on the risk of CKD.

Sequential genetic testing of living-related donors for inherited renal disease to promote informed choice and enhance safety of living donation

Living kidney donors (LKDs) with a family history of renal disease are at risk of kidney disease as compared to LKDs without such history suggesting that some LKDs may be pre-symptomatic for monogenic kidney disease. LKDs with related transplant candidates whose kidney disease was considered genetic in origin were selected for genetic testing. In each case, the transplant candidate was first tested to verify the genetic diagnosis. A genetic diagnosis was confirmed in 12 of 24 transplant candidates (ADPKD-PKD1: 6, ALPORT-COL4A3: 2, ALPORT-COL4A5: 1: nephronophthisis-SDCCAG8: 1; CAKUT-HNF1B and ADTKD-MUC1: 1 each) and 2 had variants of unknown significance (VUS) in phenotype-relevant genes. Focused genetic testing was then done in 20 of 34 LKDs. 12 LKDs screened negative for the familial variant and were permitted to donate; seven screened positive and were counseled against donation. One, the heterozygous carrier of a recessive disorder was also cleared. Six of seven LKDs with a family history of ADPKD were under 30 years and in 5, by excluding ADPKD, allowed donation to safely proceed. The inclusion of genetic testing clarified the diagnosis in recipient candidates, improving safety or informed decision-making in LKDs.

Diagnosis, Education, and Care of Patients with APOL1-Associated Nephropathy: A Delphi Consensus and Systematic Review

BACKGROUND

APOL1 variants contribute to the markedly higher incidence of ESKD in Blacks compared with Whites. Genetic testing for these variants in patients with African ancestry who have nephropathy is uncommon, and no specific treatment or management protocol for APOL1-associated nephropathy currently exists.

METHODS

A multidisciplinary, racially diverse group of 14 experts and patient advocates participated in a Delphi consensus process to establish practical guidance for clinicians caring for patients who may have APOL1-associated nephropathy. Consensus group members took part in three anonymous voting rounds to develop consensus statements relating to the following: (1) counseling, genotyping, and diagnosis; (2) disease awareness and education; and (3) a vision for management of APOL1-associated nephropathy in a future when treatment is available. A systematic literature search of the MEDLINE and Embase databases was conducted to identify relevant evidence published from January 1, 2009 to July 14, 2020.

RESULTS

The consensus group agreed on 55 consensus statements covering such topics as demographic and clinical factors that suggest a patient has APOL1-associated nephropathy, as well as key considerations for counseling, testing, and diagnosis in current clinical practice. They achieved consensus on the need to increase awareness among key stakeholders of racial health disparities in kidney disease and of APOL1-associated nephropathy and on features of a successful education program to raise awareness among the patient community. The group also highlighted the unmet need for a specific treatment and agreed on best practice for management of these patients should a treatment become available.

CONCLUSIONS

A multidisciplinary group of experts and patient advocates defined consensus-based guidance on the care of patients who may have APOL1-associated nephropathy.

Cases in Precision Medicine: Genetic Testing to Predict Future Risk for Disease in a Healthy Patient

Genetic testing is performed more routinely in clinical practice, and direct-to-consumer tests are widely available. It has obvious appeal as a preventive health measure. Clinicians and their healthy patients increasingly inquire about genetic testing as a tool for predicting diseases, such as cancer, heart disease, or dementia. Despite demonstrated utility for diagnosis in the setting of many diseases, genetic testing still has many limitations as a predictive tool for healthy persons. This article uses a hypothetical case to review key considerations for predictive genetic testing.

Novel genetic testing model: A collaboration between genetic counselors and nephrology

Many barriers to genetic testing currently exist which delay or prevent diagnosis. These barriers include wait times, staffing, education, and cost. Specialists are able to identify patients with disease that may need genetic testing, but lack the genetics support to facilitate that testing in the most cost, time, and medically effective manner. The Nephrology Division and the Genetic Testing Stewardship Program at Nemours A.I. duPont Hospital for Children created a novel service delivery model in which nephrologists and genetic counselors collaborate in order to highlight their complementary strengths (clinical expertise of nephrologists and genetics and counseling skills of genetic counselors). This collaboration has reduced many barriers to care for our patients. This workflow facilitated the offering of genetic testing to 76 patients, with 86 tests completed over a 20-month period. Thirty-two tests were deferred. Twenty-seven patients received a diagnosis, which lead to a change in their medical management, three of whom were diagnosed by cascade family testing. Forty-two patients had a negative result and 16 patients had one or more variants of uncertain significance on testing. The inclusion of genetic counselors in the workflow is integral toward choosing the most cost and time effective genetic testing strategy, as well as providing psychosocial support to families. The genetic counselors obtain informed consent, and review genetic test results and recommendations with the patient and their family. The availability of this program to our patients increased access to genetic testing and helps to provide diagnoses and supportive care.

Genetic background and transplantation outcomes: insights from genome-wide association studies

PURPOSE OF REVIEW

The current review summarizes recent advances in the genetic studies of transplantation outcomes, including new genome-wide association studies for acute rejection, allograft survival, pharmacogenomics, and common transplant comorbidities.

RECENT FINDINGS

Genetic studies of kidney transplantation outcomes have begun to address the question of genetic compatibility beyond human leukocyte antigens, including the role of genome-wide mismatches in missense variants, and the 'genomic collision' hypothesis under which the risk of rejection may be increased in recipients homozygous for loss-of-function variants with grafts from nonhomozygous donors. In recent pilot studies, missense mismatch scores for transmembrane and secreted proteins were associated with antibodies against the mismatched peptides and reduced allograft survival. A 'genomic collision' at the LIMS1 locus involving a common deletion near LIMS1 gene was associated with anti-LIMS1 antibody response and increased risk of rejection. Additional genetic factors under active investigation include genome-wide polygenic risk scores for renal function and apolipoprotein L1 risk genotypes in African-American kidney donors. Due to the heterogeneity and complexity of clinical outcomes, new genome-wide association studies for rejection, allograft survival, and specific transplant comorbidities will require larger multicenter meta-analyses.

SUMMARY

Genetic compatibilities between donor and recipient represent an important determinant of rejection and long-term allograft survival. Genetic background of transplant donors may be additionally predictive of allograft function, while recipient's genomes are likely determinant of a wide range of transplantation outcomes, from rejection susceptibility to pharmacogenetics and various comorbidities related to prolonged immunosuppression.

Using race in the estimation of glomerular filtration rates: time for a reversal?

PURPOSE OF REVIEW

Bedside estimates of renal function are essential for clinical practice in the modern era and have largely relied on serum creatinine concentrations despite the known drawbacks associated with this choice of biomarker, including the fact that creatinine clearance overestimates the glomerular filtration rate.

RECENT FINDINGS

Initial estimates relied primarily on equations that incorporated factors known to influence creatinine concentrations such as age, sex and anthropometric measures. More recent estimates of glomerular filtration rate have replaced the anthropometric measures with the social construct of race, suggesting that glomerular filtration rates for black individuals are higher at the same concentration of creatinine. This approach has led to large variations in the estimated differences in glomerular filtration rate between black and nonblack individuals in the United States that have not been reproducible, resulting in a plethora of population-specific formulae across the country.

SUMMARY

The introduction of race in estimated glomerular filtration rate equations may have potential unintended negative consequences for the very population with the greatest burden of kidney disease. These potential disadvantages underscore the need to perhaps return to the replacement of race with more objective anthropometric measures without the loss of precision.

Clinical Applications of Genetic Discoveries in Kidney Transplantation: a Review

Growth in knowledge of the genetics of kidney disease has revealed that significant percentages of patients with diverse types of nephropathy have causative mutations. Genetic testing is poised to play an increasing role in the care of patients with kidney disease. The role of genetic testing in kidney transplantation is not well established. This review will explore the ways in which genetic testing may be applied to improve the care of kidney transplant recipients and donors.