Kidney Week

Abstract: SA-PO0580

Optimizing Next-Generation Sequencing for Genetic Diagnosis in ADPKD

Session Information

• Cystic Kidney Diseases: Clinical Research
  November 08, 2025 | Location: Exhibit Hall, Convention Center
  Abstract Time: 10:00 AM - 12:00 PM

Category: Genetic Diseases of the Kidneys

• 1201 Genetic Diseases of the Kidneys: Monogenic Kidney Diseases

Authors

• Cho, Soyoung, Yale School of Medicine Department of Internal Medicine, New Haven, Connecticut, United States

Soyoung Cho

• Ma, Deqiong, Yale School of Medicine Department of Genetics, New Haven, Connecticut, United States

Deqiong Ma

• Meng, Xinmiao, Yale School of Medicine Department of Internal Medicine, New Haven, Connecticut, United States

Xinmiao Meng, MPH

• Peng, Gang, Indiana University, Department of Medical and Molecular Genetics, Bloomington, Indiana, United States

Gang Peng, PhD

• Bale, Allen E., Yale School of Medicine Department of Genetics, New Haven, Connecticut, United States

Allen E. Bale, MD

• Somlo, Stefan, Yale School of Medicine Department of Internal Medicine, New Haven, Connecticut, United States

Stefan Somlo, MD

• Besse, Whitney, Yale School of Medicine Department of Internal Medicine, New Haven, Connecticut, United States

Whitney Besse, MD

Background

Autosomal dominant polycystic kidney disease (ADPKD) affects 1:1000, causing 5-10% of kidney failure worldwide. The major ADPKD disease gene, PKD1, has six pseudogenes with 97-99% homology, a >12kb transcript, regions of high GC content and a polypyrimidine tract. Long-range PCR with Sanger sequencing has been the “gold-standard” for PKD1 testing, yet affordable next-generation sequencing gene panels have largely taken over clinical genetic testing for ADPKD prior to rigorous assessment of their performance.

Methods

We performed whole exome sequencing (WES) on 203 ADPKD patients in 171 families from the Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease (CRISP) cohort, for which the “gold standard” genetic testing was reported: n=157 PKD1, n=27 PKD2, n=19 with no mutation detected (NMD). Clinical geneticist authors, blinded to predetermined genotype, reviewed WES data. We compared pipeline modifications, exome capture reagents, and evaluated the benefit of deeper WES sequencing and whole genome sequencing (WGS) for patients that remained unsolved.

Results

We identified 150 of 157 (95.5%) of defined pathogenic variants in PKD1, 27 of 27 (100%) variants in PKD2, and solved at least 8 of 19 NMD cases using optimized analysis of WES. We characterized the vulnerabilities of a standard analysis pipeline on research-grade WES which would miss at least 22 true-positive PKD1 variants due to GATK HardFiltering or misassignment to an alternative locus. Higher-depth WES extended PKD1 variant detection to 100%. WGS identified a balanced translocation [t(1;16)(q31.1; p13.3)] in a patient previously unsolved.

Conclusion

WES can match or exceed the sensitivity of traditional long-range PCR-based approaches for variant detection in PKD1 but this requires gene-specific optimization of bioinformatic pipelines. Our findings highlight strategies to enhance sensitivity of cost-efficient and accessible next-generation sequencing for identifying disease-causing variants in ADPKD.

Funding

• NIDDK Support

Digital Object Identifier (DOI)

• doi: 10.1681/ASN.2025k70hqfkz