Diagnosis of autosomal dominant polycystic kidney disease using efficient PKD1 and PKD2 targeted next-generation sequencing

Molecular diagnostics of autosomal dominant polycystic kidney disease (ADPKD) relies on mutation screening of PKD1 and PKD2, which is complicated by extensive allelic heterogeneity and the presence of six highly homologous sequences of PKD1. To date, specific sequencing of PKD1 requires laborious long-range amplifications. The high cost and long turnaround time of PKD1 and PKD2 mutation analysis using conventional techniques limits its widespread application in clinical settings. We performed targeted next-generation sequencing (NGS) of PKD1 and PKD2. Pooled barcoded DNA patient libraries were enriched by in-solution hybridization with PKD1 and PKD2 capture probes. Bioinformatics analysis was performed using an in-house developed pipeline. We validated the assay in a cohort of 36 patients with previously known PKD1 and PKD2 mutations and five control individuals. Then, we used the same assay and bioinformatics analysis in a discovery cohort of 12 uncharacterized patients. We detected 35 out of 36 known definitely, highly likely, and likely pathogenic mutations in the validation cohort, including two large deletions. In the discovery cohort, we detected 11 different pathogenic mutations in 10 out of 12 patients. This study demonstrates that laborious long-range PCRs of the repeated PKD1 region can be avoided by in-solution enrichment of PKD1 and PKD2 and NGS. This strategy significantly reduces the cost and time for simultaneous PKD1 and PKD2 sequence analysis, facilitating routine genetic diagnostics of ADPKD.This project was funded by the Spanish Plan Nacional SAF2008-00357 (NOVADIS); the Instituto de Salud Carlos III (FIS/FEDER PI11/00733; PI12/01523 and PI13/01731); the European Commission/n7th Framework Program, Project N. 261123 (GEUVADIS), and Project N. 262055 (ESGI); Spanish Renal Network for Research 16/06, RETICS, Instituto de Investigación Carlos III: REDinREN/RD06/0016 and RD012/0021 FEDER funds; the Catalan Government (AGAUR/n2009/SGR-1116); and the Fundación Renal Iñigo Álvarez de Toledo in Spain. D. T. is a PhD student supported by the Spanish Ministry of Economy and Competiveness. R. T. is supported by Intensification Programm of Research Activity ISCIII/Generalitat de Catalunya (programm I3SN). We acknowledge support of the Spanish Ministry of Economy and Competitiveness, ‘Centro de/nExcelencia Severo Ochoa 2013-2017’, SEV-2012-0208