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Kidney Week

Abstract: TH-PO660

PKD1 Duplicated Regions Limit Clinical Utility of Whole Exome Sequencing for Genetic Diagnosis of ADPKD

Session Information

Category: Genetic Diseases of the Kidney

  • 1001 Genetic Diseases of the Kidney: Cystic

Authors

  • Ali, Hamad, Kuwait University, Jabriya, Kuwait
  • Harris, Peter C., Mayo Clinic , Rochester, Minnesota, United States

Group or Team Name

  • PKD-KWI gorup
Background

Genetic diagnosis of ADPKD is complicated by the existence of PKD1 pseudogenes located proximal to the original gene. The ability of NGS platforms in identification of ADPKD mutations, especially in the duplicated regions of PKD1, is important for potential utilization of such technologies in diagnostic applications.

Methods

We evaluate the efficiency of WES, WGS & Targeted enrichment in sequencing PKD1 and PKD2 for the detection of ADPKD mutations in patients who were clinically evaluated by ultrasonography and RFT.

Results

WES had a 50% sensitivity in detection of PKD1 mutations as the reading depth and sequencing quality were low over the duplicated regions of PKD1.

Conclusion

Our investigation highlights a major limitation of WES platform in ADPKD genetic diagnosis.

WES and Target enrichment coverage map of PKD1. WES of exons 1 to 32 of PKD1 showed low coverage while PKD2 coverage showed proper depth of all exons. Target Enrichment showed proper coverage for coding regions of PKD1 and PKD2. SureSelect v6 improved the coverage of PKD1 but in comparison to WES but exons 1 to 14 remained poorly covered. WGS showed proper covering of the entire PKD1.

WES, Target enrichment coverage map and WGS of PKD2. PKD2 was covered properly using all methods.