Diagnostic yield of massively parallel sequencing in patients with chronic kidney disease of unknown etiology: rationale and design of a national prospective cohort study

The Importance of Copy Number Variant Analysis in Patients with Monogenic Kidney Disease

Introduction

Genetic testing can reveal monogenic causes of kidney diseases, offering diagnostic, therapeutic, and prognostic benefits. Although single nucleotide variants (SNVs) and copy number variants (CNVs) can result in kidney disease, CNV analysis is not always included in genetic testing.

Methods

We investigated the diagnostic value of CNV analysis in 2432 patients with kidney disease genetically tested at the University Medical Centre Utrecht between 2014 and May 2022. We combined previous diagnostic testing results, encompassing SNVs and CNVs, with newly acquired results based on retrospective CNV analysis. The reported yield considers both the American College of Medical Genetics and Genomics (ACMG) classification and whether the genotype actually results in disease.

Results

We report a diagnostic yield of at least 23% for our complete diagnostic cohort. The total diagnostic yield based solely on CNVs was 2.4%. The overall contribution of CNV analysis, defined as the proportion of positive genetic tests requiring CNV analysis, was 10.5% and varied among different disease subcategories, with the highest impact seen in congenital anomalies of the kidney and urinary tract (CAKUT) and chronic kidney disease at a young age. We highlight the efficiency of exome-based CNV calling, which reduces the need for additional diagnostic tests. Furthermore, a complex structural variant, likely a COL4A4 founder variant, was identified. Additional findings unrelated to kidney diseases were reported in a small percentage of cases.

Conclusion

In summary, this study demonstrates the substantial diagnostic value of CNV analysis, providing insights into its contribution to the diagnostic yield and advocating for its routine inclusion in genetic testing of patients with kidney disease.

Genetic Markers Among the Israeli Druze Minority Population With End-Stage Kidney Disease

RATIONALE & OBJECTIVE

Genetic etiologies have been identified among approximately 10% of adults with chronic kidney disease (CKD). However, data are lacking regarding the prevalence of monogenic etiologies especially among members of minority groups. This study characterized the genetic markers among members of an Israeli minority group with end-stage kidney disease (ESKD).

STUDY DESIGN

A national-multicenter cross-sectional study of Israeli Druze patients (an Arabic-speaking Near-Eastern transnational population isolate) who are receiving maintenance dialysis for ESKD. All study participants underwent exome sequencing.

SETTING & PARTICIPANTS

We recruited 94 adults with ESKD, comprising 97% of the total 97 Druze individuals throughout Israel being treated with dialysis during the study period.

PREDICTORS

Demographics and clinical characteristics of kidney disease.

OUTCOME

Genetic markers.

ANALYTICAL APPROACH

Whole-exome sequencing and the relationship of markers to clinical phenotypes.

RESULTS

We identified genetic etiologies in 17 of 94 participants (18%). None had a previous molecular diagnosis. A novel, population-specific, WDR19 homozygous pathogenic variant (p.Cys293Tyr) was the most common genetic finding. Other monogenic etiologies included PKD1, PKD2, type IV collagen mutations, and monogenic forms of noncommunicable diseases. The pre-exome clinical diagnosis corresponded to the final molecular diagnosis in fewer than half of the participants.

LIMITATIONS

This study was limited to Druze individuals, so its generalizability may be limited.

CONCLUSIONS

Exome sequencing identified a genetic diagnosis in approximately 18% of Druze individuals with ESKD. These results support conducting genetic analyses in minority populations with high rates of CKD and for whom phenotypic disease specificity may be low.

PLAIN-LANGUAGE SUMMARY

Chronic kidney disease (CKD) affects many people worldwide and has multiple genetic causes. However, there is limited information on the prevalence of genetic etiologies, especially among minority populations. Our national-multicenter study focused on Israeli Druze patients. Using exome-sequencing, we identified previously undetected genetic causes in nearly 20% of patients, including a new and population-specific WDR19 homozygous pathogenic variant. This mutation has not been previously described; it is extremely rare globally but is common among the Druze, which highlights the importance of studying minority populations with high rates of CKD. Our findings provide insights into the genetic basis of end-stage kidney disease in the Israeli Druze, expand the WDR19 phenotypic spectrum, and emphasize the potential value of genetic testing in such populations.

Protective effect of Peucedanum praeruptorum Dunn extract on oxidative damage of LLC‑PK1 cells induced by H2O2

Peucedanum praeruptorum Dunn extract (PPDE) is a well-known treatment used in traditional Chinese medicines, where it is most commonly used to treat coughs and symptoms such as headaches and fever. In the present study, the antioxidant capacity of PPDE in vitro was determined by scavenging experiments using DPPH, ABTS+·, ·OH, and ·O2-. The cell survival rate was determined by MTT assay. The MDA, SOD, CAT, GSH, and GSH-Px content were determined by colorimetry assays. The expression levels of antioxidant genes SOD, CAT, GSH, and GSH-Px were assessed by reverse transcription-quantitative PCR. HPLC was used to identify the PPDE components. The results suggested that PPDE had scavenging effects on DPPH, ABTS, hydroxyl, and superoxide anion radicals in a concentration-dependent manner; H2O2 treatment resulted in oxidative stress in LLC-PK1 cells, and the degree of injury of LLC-PK1 cells following PPDE treatment was improved, which was positively correlated with its concentration. Peucedanum praeruptorum Dunn extract treatment reduced the content of MDA and increased the content of CAT, SOD1, GSH, and GSH-Px. The mRNA expression levels of antioxidant genes detected by quantitative PCR were consistent with changes in CAT, SOD, GSS, and GSH-Px. Additionally, the trend in CAT, SOD1, GSH, and GSS protein expression levels was also consistent at the mRNA level. PPDE was found to consist of isochlorogenic acid C, myricetin, baicalin, luteolin, and kaempferol. Therefore, PPDE, which was formed of products derived from natural substances, functioned in the inhibition of oxidative damage. The present study aimed to obtain a better understanding of the traditional Chinese medicine Peucedanum praeruptorum Dunn and preliminarily elucidate its antioxidant mechanism at the cellular level. Further animal or human experiments are required to verify the antioxidant effects of PPDE for further development and utilization.

Which patients with CKD will benefit from genomic sequencing? Synthesizing progress to illuminate the future

PURPOSE OF REVIEW

This review will summarize and synthesize recent findings in regard to monogenic kidney disorders, including how that evidence is being translated into practice. It will add to existing key knowledge to provide context for clinicians in consolidating existing practice and approaches.

RECENT FINDINGS

Whilst there are long established factors, which indicate increased likelihood of identifying a monogenic cause for kidney disease, these can now be framed in terms of the identification of new genes, new indications for genomic testing and new evidence for clinical utility of genomic testing in nephrology. Further, inherent in the use of genomics in nephrology are key concepts including robust informed consent, variant interpretation and return of results. Recent findings of variants in genes related to complex or broader kidney phenotypes are emerging in addition to understanding of de novo variants. Phenocopy phenomena are indicating a more pragmatic use of broader gene panels whilst evidence is emerging of a role in unexplained kidney disease. Clinical utility is evolving but is being successfully demonstrated across multiple domains of outcome and practice.

SUMMARY

We provide an updated framework of evidence to guide application of genomic testing in chronic kidney disease (CKD), building upon existing principles and knowledge to indicate how the practice and implementation of this can be applied today. There are clearly established roles for genomic testing for some patients with CKD, largely those with suspected heritable forms, with these continuing to expand as new evidence emerges.