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

Nephrologists' Views on a Workflow for Returning Genetic Results to Research Participants

Introduction

Returning research-based genetic results (gRoR) to participants in nephrology research can improve care; however, the practice raises implementational questions and no established guidelines for this process currently exist. Nephrologists' views on this issue can inform the process but are understudied.

Methods

We developed a conceptual workflow for gRoR from literature and experience, covering aspects such as which results to return, how, and by whom. We surveyed US nephrologists to gauge their views on the workflow and anticipated barriers and collected participants' demographics, including professional backgrounds.

Results

A total of 201 adult and pediatric nephrologists completed the survey. Most of them agreed that all diagnostic kidney-related results (93%), secondary findings (80%), and kidney-related risk variants (83%) should be returned. No significant differences were found between adult and pediatric nephrologists' responses, except that 48% of adult nephrologists versus 26% of pediatric nephrologists supported returning polygenic risk scores (PRS) (P < 0.01). Seventy-nine percent wanted to know about research results before clinical confirmation. Most of them (63%) believed a genetic counselor should return clinically confirmed results. Key barriers included the cost of clinical validation (77%) and the unavailability of genetic counseling services (63%). Facilitators included educational resources on genetic kidney diseases (91%), a referral list of experts (89%), and clear clinical care guidelines (89%). We discuss findings' implications and provide "points to consider."

Conclusion

There is significant interest in gRoR among nephrologists; however, logistical and economic concerns need addressing. Identified facilitators can help large nephrology studies planning to return genetic results to participants.

Review of childhood genetic nephrolithiasis and nephrocalcinosis

Nephrolithiasis (NL) is a common condition worldwide. The incidence of NL and nephrocalcinosis (NC) has been increasing, along with their associated morbidity and economic burden. The etiology of NL and NC is multifactorial and includes both environmental components and genetic components, with multiple studies showing high heritability. Causative gene variants have been detected in up to 32% of children with NL and NC. Children with NL and NC are genotypically heterogenous, but often phenotypically relatively homogenous, and there are subsequently little data on the predictors of genetic childhood NL and NC. Most genetic diseases associated with NL and NC are secondary to hypercalciuria, including those secondary to hypercalcemia, renal phosphate wasting, renal magnesium wasting, distal renal tubular acidosis (RTA), proximal tubulopathies, mixed or variable tubulopathies, Bartter syndrome, hyperaldosteronism and pseudohyperaldosteronism, and hyperparathyroidism and hypoparathyroidism. The remaining minority of genetic diseases associated with NL and NC are secondary to hyperoxaluria, cystinuria, hyperuricosuria, xanthinuria, other metabolic disorders, and multifactorial etiologies. Genome-wide association studies (GWAS) in adults have identified multiple polygenic traits associated with NL and NC, often involving genes that are involved in calcium, phosphorus, magnesium, and vitamin D homeostasis. Compared to adults, there is a relative paucity of studies in children with NL and NC. This review aims to focus on the genetic component of NL and NC in children.

Genetic testing in the evaluation of recipient candidates and living kidney donors

PURPOSE OF REVIEW

The aim of this study is to provide an overview of the role of genetic testing in the evaluation of kidney transplant candidates and living donors who may be at risk for heritable kidney disease. We focus our discussion on monogenic diseases, excluding renal diseases that have complex polygenic influences. Adoption of new technologies such as next-generation sequencing (NGS) with comprehensive gene panels has greatly enabled access to genetic testing recently; yet transplant professionals rarely receive adequate training in clinical genetics. In addition to a broad discussion of genetic testing, we hope to illustrate the thought processes and resources used in clinical genetic evaluation of recipient candidates and donors.

RECENT FINDINGS

Targeted renal genetic panels, whole exome and genome sequencing have greatly expanded our ability to test for pathogenic variants. Testing methods, analytic tools and the subsequent interpretation by the testing laboratory and treating physician impacts patient management and clinicians may lack the resources to practice in this new era of genomic medicine.

SUMMARY

The expansion of genomics into transplant medicine can provide improved diagnosis in transplant candidates and potentially disease prediction in living donors. Transplant professionals need to be familiar with emerging trends, promises and limitations of NGS-based testing.

Future Frontiers: Exploration of practices, challenges, and educational needs of genetic counselors in emerging subspecialties

The augmented use of genomic testing across different medical subspecialties has led to increased involvement of genetic counselors (GCs) in specialized areas of medicine. However, the lack of educational infrastructure required for changing scholastic needs of GCs entering new subspecialties lends to the burden of self-directed learning and inconsistent knowledge. We conducted a cross-sectional study surveying GCs with experience in the emerging genetic subspecialties of Immunology, Dermatology, Endocrinology, and Pulmonology (abbreviated as "IDEP") on current practices, clinical challenges, and educational strategies undertaken while working in these settings. We compared knowledge and confidence in skills related to IDEP patient care between GCs who do (experienced cohort) and do not (control cohort) practice in these settings to assess their comfort with working in subspecialties. Participants were recruited from the National Society of Genetic Counselors membership. A total of 304 GCs (178 experienced and 126 control) completed the survey. Most GCs in the experienced cohort saw IDEP patients by themselves (n = 104; 58.4%) or with a geneticist (n = 97; 54.4%) and almost all (n = 176; 99%) cited GeneReviews as a primary informational source for IDEP genetics but half (n = 91; 51.1%) agreed that a dedicated online course would be the best way to learn about a specific subspecialty. The experienced cohort scored higher on confidence in all skills (p < 0.001, z = 7.32) and knowledge (p < 0.001, z = 5.68) related to IDEP genetics than the control cohort. Previous exposure to IDEP through graduate school coursework and rotations positively correlated with better self-confidence in skills (p = 0.02, z = -2.19; p < 0.001, z = -5.25) and genetic knowledge (p = 0.03, z = -2.09; p < 0.001, z = -2.81) related to IDEP patient care. Years of experience working as a GC did not correlate with better confidence in skills (p = 0.53) or better IDEP genetic knowledge (p = 0.15). Our findings show that provision of opportunities for increased exposure to subspecialties could help maximize GCs' ability to work in emerging niche fields.

Genetic testing in children with nephrolithiasis and nephrocalcinosis

BACKGROUND

Diagnosing genetic kidney disease has become more accessible with low-cost, rapid genetic testing. The study objectives were to determine genetic testing diagnostic yield and examine predictors of genetic diagnosis in children with nephrolithiasis/nephrocalcinosis (NL/NC).

METHODS

This retrospective multicenter cross-sectional study was conducted on children ≤ 21 years old with NL/NC from pediatric nephrology/urology centers that underwent the Invitae Nephrolithiasis Panel 1/1/2019-9/30/2021. The diagnostic yield of the genetic panel was calculated. Bivariate and multiple logistic regression were performed to assess for predictors of positive genetic testing.

RESULTS

One hundred and thirteen children (83 NL, 30 NC) from 7 centers were included. Genetic testing was positive in 32% overall (29% NL, 40% NC) with definite diagnoses (had pathogenic variants alone) made in 11.5%, probable diagnoses (carried a combination of pathogenic variants and variants of uncertain significance (VUS) in the same gene) made in 5.4%, and possible diagnoses (had VUS alone) made in 15.0%. Variants were found in 28 genes (most commonly HOGA1 in NL, SLC34A3 in NC) and 20 different conditions were identified. Compared to NL, those with NC were younger and had a higher proportion with developmental delay, hypercalcemia, low serum bicarbonate, hypophosphatemia, and chronic kidney disease. In multivariate analysis, low serum bicarbonate was associated with increased odds of genetic diagnosis (β 2.2, OR 8.7, 95% CI 1.4-54.7, p = 0.02).

CONCLUSIONS

Genetic testing was high-yield with definite, probable, or possible explanatory variants found in up to one-third of children with NL/NC and shows promise to improve clinical practice. A higher resolution version of the Graphical abstract is available as Supplementary information.

Genetic Counseling in Kidney Disease: A Perspective

As genetic testing is increasingly integrated into nephrology practice there is a growing need for partnership with genetic experts. Genetic counselors are ideally suited to fill this role. The value of genetic counseling is born out of the clinical value of genetic test results against the backdrop of the complexity of genetic testing. Genetic counselors who specialize in nephrology are trained to understand and explain the potential effects of genes on kidney disease, which can enable patients to make informed decisions about proceeding with genetic testing, navigating variants of uncertain significance, educating on extrarenal features of hereditary kidney disease, facilitating cascade testing, providing post-test education about testing results, and assisting with family planning. Genetic counselors can partner with the nephrologist and provide the knowledge needed to maximize the use of genetic testing for patients for nephrology consultation. Genetic counseling is more than an element or extension of genetic testing; it is a dynamic, shared conversation between the patient and the genetic counselor where concerns, sentiments, information, and education are exchanged, and value-based decision making is facilitated.

Access to clinically indicated genetic tests for pediatric patients with Medicaid: Evidence from outpatient genetics clinics in Texas

PURPOSE

Little is known about how Medicaid coverage policies affect access to genetic tests for pediatric patients. Building upon and extending a previous analysis of prior authorization requests (PARs), we describe expected coverage of genetic tests submitted to Texas Medicaid and the PAR and diagnostic outcomes of those tests.

METHODS

We retrospectively reviewed genetic tests ordered at 3 pediatric outpatient genetics clinics in Texas. We compared Current Procedural Terminology (CPT) codes with the Texas Medicaid fee-for-service schedule (FFSS) to determine whether tests were expected to be covered by Medicaid. We assessed completion and diagnostic yield of commonly ordered tests.

RESULTS

Among the 3388 total tests submitted to Texas Medicaid, 68.9% (n = 2336) used at least 1 CPT code that was not on the FFSS and 80.7% (n = 2735) received a favorable PAR outcome. Of the tests with a CPT code not on the FFSS, 60.0% (n = 1400) received a favorable PAR outcome and were completed and 20.5% (n = 287) were diagnostic. The diagnostic yield of all tests with a favorable PAR outcome that were completed was 18.7% (n = 380/2029).

CONCLUSION

Most PARs submitted to Texas Medicaid used a CPT code for which reimbursement from Texas Medicaid was not guaranteed. The frequency with which clinically indicated genetic tests were not listed on the Texas Medicaid FFSS suggests misalignment between genetic testing needs and coverage policies. Our findings can inform updates to Medicaid policies to reduce coverage uncertainty and expand access to genetic tests with high diagnostic utility.

Incorporating genetics services into adult kidney disease care

Studies have shown that as many as 1 in 10 adults with chronic kidney disease has a monogenic form of disease. However, genetic services in adult nephrology are limited. An adult Kidney Genetics Clinic was established within the nephrology division at a large urban academic medical center to increase access to genetic services and testing in adults with kidney disease. Between June 2019 and December 2021, a total of 363 patients were referred to the adult Kidney Genetics Clinic. Of those who completed genetic testing, a positive diagnostic finding was identified in 27.1%, a candidate diagnostic finding was identified in 6.7% of patients, and a nondiagnostic positive finding was identified in an additional 8.6% of patients, resulting in an overall yield of 42.4% for clinically relevant genetic findings in tested patients. A genetic diagnosis had implications for medical management, family member testing, and eligibility for clinical trials. With the utilization of telemedicine, genetic services reached a diverse geographic and patient population. Genetic education efforts were integral to the clinic's success, as they increased visibility and helped providers identify appropriate referrals. Ongoing access to genomic services will remain a fundamental component of patient care in adults with kidney disease.

Review of genetic testing in kidney disease patients: Diagnostic yield of single nucleotide variants and copy number variations evaluated across and within kidney phenotype groups

Genetic kidney disease comprises a diverse group of disorders. These can roughly be divided in the phenotype groups congenital anomalies of the kidney and urinary tract, ciliopathies, glomerulopathies, stone disorders, tubulointerstitial kidney disease, and tubulopathies. Many etiologies can lead to chronic kidney disease that can progress to end-stage kidney disease. Despite each individual disease being rare, together these genetic disorders account for a large proportion of kidney disease cases. With the introduction of massively parallel sequencing, genetic testing has become more accessible, but a comprehensive analysis of the diagnostic yield is lacking. This review gives an overview of the diagnostic yield of genetic testing across and within the full range of kidney disease phenotypes through a systematic literature search that resulted in 115 included articles. Patient, test, and cohort characteristics that can influence the diagnostic yield are highlighted. Detection of copy number variations and their contribution to the diagnostic yield is described for all phenotype groups. Also, the impact of a genetic diagnosis for a patient and family members, which can be diagnostic, therapeutic, and prognostic, is shown through the included articles. This review will allow clinicians to estimate an a priori probability of finding a genetic cause for the kidney disease in their patients.

Impact of Genetic Testing on Human Health:

Advances in the field of human genetics over the past three decades have led to improvements in human health through development and availability of novel genetic testing approaches for diagnosis, prognosis, treatment therapy, safety, preventive screening and population-based risk assessment. In this commentary, I highlight the current landscape of genetic testing in Delaware with a focus on the genetic etiology and molecular diagnosis of pediatric disease, tailored treatment efficacy and safety through novel clinical trials and pharmacogenomics, and training in the application of genomic approaches to rare and common diseases. Future opportunities include integrating application of genetic information into clinical practice, improving genetics education, focusing on disparities and access, and advancing genomics and digital health technologies.

Molecular Genetic Testing for Kidney Disorders During the COVID-19 Pandemic

Chronic kidney disease (CKD) has major morbidity and mortality for children and adults. While in adults CKD often is associated with diabetic complications, genetic variants can be the underlying cause in both populations. Beginning in 2016 with the emergence of more affordable next-generation sequencing (NGS) technologies, the Molecular Diagnostics Lab at Nemours Children’s Hospital-Delaware developed the first clinically actionable pediatric NGS kidney panel comprised of 46 genes including APOL1. Apolipoprotein L1 (APOL1) associated nephropathy is reported along a spectrum of non-diabetic kidney disease. It is significantly associated with two “risk alleles” defined as G1 and G2 and typically found in individuals of African descent. In early 2020, as COVID-19 spread across the globe, reports of patients with kidney failure began to emerge. A collapsing glomerulopathy in Black patients with COVID-19 was found to be associated with the APOL1 predisposition of the known G1 and/or G2 risk variants. We identified genetic variants in 11 genes (NPHS1; NPHS2; LAMB2; WT1; COL4A4; COL4A5; COQ8B; CUBN; MEFV; PMM2; SMARCAL1) known to be associated with pediatric onset nephrotic syndrome, or detection of the high-risk haplotype of APOL1, in the majority (78%) of patients tested. These clinically actionable results guided medical care and improved patient outcomes.