Genetics of ADPKD : using long-range PCR to complement whole exome sequencing data

Abstract

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most common inherited kidney disease. It is characterized by the progressive development of renal cysts. The 2 main genes implicated in ADPKD are Polycystin 1, Transient Receptor Potential Channel Interacting (PKD1) and Polycystin 2, Transient Receptor Potential Cation Channel (PKD2). Other recent novel genes which have been implicated in ADPKD are Glucosidase II Alpha Subunit (GANAB) and Alpha-1,2-Mannosyltransferase (ALG9). In an ongoing whole exome sequencing (WES) study of local ADPKD patients, no pathogenic variants were identified in two of the cases. Assessment of genomic data indicated that certain exons of PKD1 and PKD2 were not suitably captured during library preparation and thus there is missing data for these exons. Coverage analysis showed that data was missing from 10 PKD1 and 5 PKD2 exons. Analysis of whole exome sequencing (WES) data with a lower coverage cut-off of 20x recovered data for 3 PKD1 and 3 PKD2 exons. PCR and Sanger sequencing analysis generated data for a further 2 PKD1 and 1 PKD2 exons. An additional 26 DNA variants were identified in PKD1 and PKD2 in patient DNA. Of these, 15 were coding variants, 3 of which were classified as pathogenic or likely pathogenic. These results show that low coverage of HTS data may be the cause of no variants identified in ADPKD patients.