A Low-Cost Sequencing Platform for Rapid Genotyping in ADPKD and its Impact on Clinical Care

Christoph Heinrich Lindemann; Andrea Wenzel; Florian Erger; Lea Middelmann; Julika Borde; Eric Hahnen; Denise Krauß; Simon Oehm; Sita Arjune; Polina Todorova; Kathrin Burgmaier; Max Christoph Liebau; Franziska Grundmann; Bodo B Beck; Roman-Ulrich Müller

doi:10.1016/j.ekir.2022.12.025

A Low-Cost Sequencing Platform for Rapid Genotyping in ADPKD and its Impact on Clinical Care

Kidney Int Rep. 2022 Dec 28;8(3):455-466. doi: 10.1016/j.ekir.2022.12.025. eCollection 2023 Mar.

Authors

Christoph Heinrich Lindemann¹, Andrea Wenzel², Florian Erger^{2

3

4}, Lea Middelmann², Julika Borde⁵, Eric Hahnen⁵, Denise Krauß¹, Simon Oehm¹, Sita Arjune¹, Polina Todorova¹, Kathrin Burgmaier^{6

7}, Max Christoph Liebau⁸, Franziska Grundmann¹, Bodo B Beck^{2

3

4}, Roman-Ulrich Müller^{1

9}

Affiliations

¹ University of Cologne, Faculty of Medicine and University Hospital Cologne, Department 2 of Internal Medicine, Cologne, Germany.
² Institute of Human Genetics, University Hospital Cologne, Faculty of Medicine, University of Cologne, Cologne, Germany.
³ Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.
⁴ Center for Rare Diseases Cologne, University Hospital Cologne, Faculty of Medicine, University of Cologne, Cologne, Germany.
⁵ Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
⁶ Department of Pediatrics, University Hospital Cologne and Faculty of Medicine, University of Cologne, Cologne, Germany.
⁷ Faculty of Applied Healthcare Science, Deggendorf Institute of Technology, Deggendorf, Germany.
⁸ Department of Pediatrics, Center for Family Health, Center for Rare Diseases Cologne and Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
⁹ Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany.

Abstract

Introduction: Autosomal-dominant polycystic kidney disease (ADPKD) is the most common genetic cause of kidney failure. Because of the heterogeneity in disease progression in ADPKD, parameters predicting future outcome are important. The disease-causing genetic variant is one of these parameters.

Methods: A multiplex polymerase chain reaction (PCR)-based panel (MPP) was established for analysis of 6 polycystic kidney disease (PKD) genes (PKD1, PKD2, HNF1B, GANAB, DZIP1L, and PKHD1) in 441 patients with ADPKD. Selected patients were additionally sequenced using Sanger sequencing or a custom enrichment-based gene panel. Results were combined with clinical characteristics to assess the impact of genetic data on clinical decision-making. Variants of unclear significance (VUS) were considered diagnostic based on a classic ADPKD clinical phenotype.

Results: Using the MPP, disease-causing variants were detected in 65.3% of patients. Sanger sequencing and the custom gene panel in 32 patients who were MPP-negative revealed 20 variants missed by MPP, (estimated overall false negative rate 24.6%, false-positive rate 9.4%). Combining clinical and genetic data revealed that knowledge of the genotype could have impacted the treatment decision in 8.2% of patients with a molecular genetic diagnosis. Sequencing only the PKD1 pseudogene homologous region in MPP-negative patients resulted in an acceptable false-negative rate of 3.28%.

Conclusion: The MPP yields rapid genotype information at lower costs and allows for simple extension of the panel for new disease genes. Additional sequencing of the PKD1 pseudogene homologous region is required in negative cases. Access to genotype information even in settings with limited resources is important to allow for optimal patient counseling in ADPKD.

Keywords: ADPKD; CKD; PKD; Sanger sequencing; next generation sequencing.