A labor and cost effective next generation sequencing of PKHD1 in autosomal recessive polycystic kidney disease patients

•We optimized a next generation sequencing procedure for PKHD1.•Five DNA pools of polycystic kidney disease patients were Next generation sequenced.•Putative mutations were assigned to specific patients through Sanger sequencing.•At least one mutation was identified in 20 of the 22 cases.•The procedure was cost and labor saving compared to other sequencing approaches.

The Sanger sequencing of patients with recessive polycystic kidney disease is challenging due to the length and heterogeneous mutational spectrum of the PKHD1 gene. Next generation sequencing (NGS) might thus be of special interest to search for PKHD1 mutations. The study involved a total of 22 patients with autosomal recessive polycystic kidney disease (ARPKD) and 8 parents of non-available ARPKD patients. Five pools of 6 samples each were sequenced with the Personal Genome Machine (PGM, Ion Torrent). For each DNA pool, a total of 109 fragments that covered the entire PKHD1 coding sequence were amplified in only two tubes followed by library preparation and NGS with the PGM. To validate the technique, each pool contained the DNA of at least one patient with known mutation. The putative mutations identified in each pool were confirmed and assigned to specific individuals through Sanger sequencing.All but one of the 109 amplicons were successfully read, and we identified the two PKHD1 mutations in 11 of the ARPKD cases, one mutation in 9 patients, and no mutation in only 2 patients. Six of the 8 parents from non-available patients were mutation carriers.The reported procedure would facilitate the large scale analysis of PKHD1 with a significant reduction in cost and labor.