Somatic mutation in autosomal dominant polycystic kidney disease revealed by deep sequencing human kidney cysts

Abstract

Autosomal Dominant Polycystic Kidney Disease (ADPKD) results in progressive cysts that lead to kidney failure, and is caused by heterozygous germline variants in PKD1 or PKD2. Cyst pathogenesis is not definitively understood. Somatic second-hit mutations have been implicated in cyst pathogenesis, though technical sequencing challenges have limited investigation. We used unique molecular identifiers, high-depth massively parallel sequencing and custom analysis techniques to identify somatic second-hit mutations in 24 whole cysts from disparate regions of six human ADPKD kidneys, utilising replicate samples and orthogonal confirmation. Average depth of coverage of 1166 error-corrected reads for PKD1 and 539 reads for PKD2 was obtained. 58% (14/24) of cysts had a detectable PKD1 somatic variant, with 5/6 participants having at least one cyst with a somatic variant. We demonstrate that low-frequency somatic mutations are detectable in a proportion of cysts from end-stage ADPKD human kidneys. Further studies are required to understand the drivers of this somatic mutation.

Fig. 1. Study Method.

Method for sample collection, processing, sequencing and analysis. Inset A Representative photograph of nephrectomy sample, includes 30 cm ruler for reference. Inset B Representative images of single cyst samples after dissection. Graduation of ruler is 1 mm.

Fig. 2. Somatic and germline variants identified.

Main figure: Lollipop diagram of somatic second hit variants identified across the PKD1 gene. ‘Lollipops’ on the top represent somatic variants and ‘Lollipops’ underneath represent germline variants. Insets: Demonstrate representative data of the sequence reads that supported the somatic variants identified, with original cyst sample data, data from replicate cyst sample and data from sequencing of blood. Diagram developed with ProteinPaint. PKD1 NM_001009944.3.