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Somatic mutation in autosomal dominant polycystic kidney disease revealed by deep sequencing human kidney cysts
Amali C Mallawaarachchi1,2,3,4, Yvonne Hort5, Laura Wedd5,6,7
1Molecular Genetics of Inherited Kidney Disorders Laboratory, Garvan Institute of Medical Research, Sydney, NSW, Australia. a.mallawaarachchi@garvan.org.au.
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.
Insights
Somatic mutations in PKD1 were found in over half of Autosomal Dominant Polycystic Kidney Disease (ADPKD) cysts, suggesting a role in disease progression. These findings advance our understanding of ADPKD cyst development.
Area of Science:
- Genetics
- Nephrology
- Molecular Biology
Background:
- Autosomal Dominant Polycystic Kidney Disease (ADPKD) is a genetic disorder characterized by progressive kidney cyst formation leading to renal failure.
- The precise mechanisms driving cyst pathogenesis in ADPKD remain incompletely understood.
- Somatic second-hit mutations in PKD1 or PKD2 have been hypothesized to contribute to cyst development, but investigation has been limited by technical challenges.
Purpose of the Study:
- To investigate the presence and frequency of somatic second-hit mutations in PKD1 and PKD2 within human ADPKD kidney cysts.
- To overcome technical sequencing limitations to accurately detect low-frequency somatic mutations in ADPKD cysts.
Main Methods:
- Utilized unique molecular identifiers (UMIs) and high-depth massively parallel sequencing for sensitive mutation detection.
- Employed custom analysis techniques and orthogonal confirmation for robust identification of somatic variants.
- Analyzed 24 whole cysts from six human ADPKD kidneys, with replicate samples for validation.
Main Results:
- Achieved high average depths of coverage: 1166 error-corrected reads for PKD1 and 539 for PKD2.
- Detected detectable somatic PKD1 variants in 58% (14/24) of analyzed cysts.
- Found at least one cyst with a somatic variant in 5 out of 6 participants, indicating widespread occurrence.
Conclusions:
- Demonstrated the detectability of low-frequency somatic mutations in a significant proportion of cysts from end-stage human ADPKD kidneys.
- These findings provide evidence for the role of somatic mutations in ADPKD cystogenesis.
- Further research is warranted to elucidate the specific drivers and functional consequences of these somatic mutations in ADPKD pathogenesis.
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