Exome sequencing of Saudi Arabian patients with ADPKD

Abstract

Purpose: Autosomal dominant polycystic kidney disease (ADPKD) is characterized by progressive development of kidney cysts and enlargement and dysfunction of the kidneys. The Consortium of Radiologic Imaging Studies of the Polycystic Kidney Disease (CRISP) cohort revealed that 89.1% had either a PKD1 or PKD2 mutation. Of the CRISP patients with a genetic cause detected, mutations in PKD1 accounted for 85%, while mutations in the PKD2 accounted for the remaining 15%. Here, we report exome sequencing of 16 Saudi patients diagnosed with ADPKD and 16 ethnically matched controls. Methods: Exome sequencing was performed using combinatorial probe-anchor synthesis and improved DNA Nanoballs technology on BGISEQ-500 sequencers (BGI, China) using the BGI Exome V4 (59 Mb) Kit. Identified variants were validated with Sanger sequencing. Results: With the exception of GC-rich exon 1, we obtained excellent coverage of PKD1 (mean read depth ¼ 88) including both duplicated and non-duplicated regions. Of nine patients with typical ADPKD presentations (bilateral symmetrical kidney involvement, positive family history, concordant imaging, and kidney function), four had protein truncating PKD1 mutations, one had a PKD1 missense mutation, and one had a PKD2 mutation. These variants have not been previously observed in the Saudi population. In seven clinically diagnosed ADPKD cases but with atypical features, no PKD1 or PKD2 mutations were identified, but rare predicted pathogenic heterozygous variants were found in cystogenic candidate genes including PKHD1, PKD1L3, EGF, CFTR, and TSC2. Conclusions: Mutations in PKD1 and PKD2 are the most common cause of ADPKD in Saudi patients with typical ADPKD.

Novel method for the genomic analysis of PKD1 mutation in autosomal dominant polycystic kidney disease

“…PKD1 is a large gene with 46 exons located on chromosome 16 (16p13.3) ( Consortium, 1994 ). There are six PKD1 pseudogenes ( PKDP1-P6 ) on chromosome 16 that have been six times and share high homology with PKD1 ( Bogdanova et al, 2001 ; Martin et al, 2004 ; Payne et al, 2021 ), and the GC content of some of these sequences is high ( Al-Muhanna et al, 2019 ). NGS sequencing alone has a poor capture efficiency for high-GC-content regions, resulting in some PKD1 gene mutations being undetected.…”

“…This study is the first to combine MPCR amplification with targeted region sequencing (with an effective sequencing depth of 10,000×) to accurately detect suspected pathogenic sites. At present, there are many regions of PKD1 gene with high GC, but few areas that can’t be detected by next-generation sequencing ( Al-Muhanna et al, 2019 ). Therefore, mPCR could basically cover key areas, which is a good supplementary experiment.…”

Visual inspection reveals a novel pathogenic mutation inPKD1missed by the variant caller in whole‑exome sequencing

“…To the best of our knowledge, however, the diagnostic ability of WES for PKD1 is still uncertain. Al-Muhanna et al ( 44 ) reported that 100% coverage of PKD1 is possible with WES, whereas Ali et al ( 14 ) reported poor coverage of PKD1 at duplicated regions. The difference in reported sensitivity of WES may be due to different capture kits and data analysis methods.…”

Case report: Biochemical and clinical phenotypes caused by cysteine substitutions in the epidermal growth factor-like domains of fibrillin-1

“…Raw reads generated by the sequencer were first screened and low-quality reads were discarded. Detailed data analysis and candidate gene mutation filtering criteria have been previously described ( Al-Muhanna et al, 2019 ).…”