Comprehensive Molecular Diagnostics in Autosomal Dominant Polycystic Kidney Disease

Abstract

Mutation-based molecular diagnostics of autosomal dominant polycystic kidney disease (ADPKD) is complicated by genetic and allelic heterogeneity, large multi-exon genes, duplication of PKD1, and a high level of unclassified variants (UCV). Present mutation detection levels are 60 to 70%, and PKD1 and PKD2 UCV have not been systematically classified. This study analyzed the uniquely characterized Consortium for Radiologic Imaging Study of PKD (CRISP) ADPKD population by molecular analysis. A cohort of 202 probands was screened by denaturing HPLC, followed by direct sequencing using a clinical test of 121 with no definite mutation (plus controls). A subset was also screened for larger deletions, and reverse transcription-PCR was used to test abnormal splicing. Definite mutations were identified in 127 (62.9%) probands, and all UCV were assessed for their potential pathogenicity. The Grantham Matrix Score was used to score the significance of the substitution and the conservation of the residue in orthologs and defined domains. The likelihood for aberrant splicing and contextual information about the UCV within the patient (including segregation analysis) was used in combination to define a variant score. From this analysis, 44 missense plus two atypical splicing and seven small in-frame changes were defined as probably pathogenic and assigned to a mutation group. Mutations were thus defined in 180 (89.1%) probands: 153 (85.0%) PKD1 and 27 (15.0%) PKD2. The majority were unique to a single family, but recurrent mutations accounted for 30.0% of the total. A total of 190 polymorphic variants were identified in PKD1 (average of 10.1 per patient) and eight in PKD2. Although nondefinite mutation data must be treated with care in the clinical setting, this study shows the potential for molecular diagnostics in ADPKD that is likely to become increasingly important as therapies become available. 18: 214318: -216018: , 200718: . doi: 10.1681 Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease, with an incidence of 1 in 400 to 1000 (accounting for approximately 5% of ESRD), and is characterized by the development and progressive enlargement of cysts in the kidney. ADPKD is genetically heterogeneous, with two genes identified: PKD1 (16p13.3) and PKD2 (4q21). [1][2][3][4] In linkagecharacterized populations, PKD1 accounts for approximately 85% of cases and PKD2 accounts for most of the remainder, 5,6 but further heterogeneity is possible. 7 PKD1 has an average age at ESRD of 54.3 yr, compared with 74.0 yr for PKD2. 8 PKD1 and PKD2 encode polycystin-1 (PC1) and polycystin-2 (PC2), respectively. PC2 is a TRP channel that may be involved in regulating intracellular Ca 2ϩ . 9,10 PC1 and PC2 interact and, similar to other cystogenic proteins, have been localized to primary cilia. 11,12 This complex may act as a flow-dependent mechanosensor that regulates the differentiated state of tubular epithelial cells. 13 The diagnosis of ADPKD is typically determined by renal imaging wit...

Refining Genotype-Phenotype Correlation in Autosomal Dominant Polycystic Kidney Disease

“…However, the CRISP was designed to enrich patients at high risk for renal disease progression, whereas Genkyst was enriched with probands with advanced CKD. 12,15 Thus, the latter studies displayed a spectrum of mutations associated with more severe renal disease, whereas our study provides estimates that are likely more representative of the general population.…”

“…By contrast, the reported prevalence of PKD1 PT and IF indel mutations, PKD1 NT mutations, and PKD2 mutations was 59.5%, 25.5%, and 15% in the CRISP 12 and 58.6%, 22.9%, and 18.5% in the Genkyst Study. 15 Compared with the two latter studies, we found a lower prevalence of PKD1 PT and IF indel mutations, which are associated with severe renal disease, and a higher prevalence of PKD2 mutations, which are associated with mild renal disease.…”

“…12 Comprehensive screening for PKD1 mutations is now possible using protocols that exploit rare mismatches between its duplicated region and the pseudogenes using PKD1-specific PCR. 12 With this advance, the Consortium for Radiologic Imaging Study of PKD (CRISP) reported a comprehensive survey of the spectrum of PKD1 and PKD2 mutations in 180 patients. 12 Among the putative deleterious PKD1 variants identified in 153 patients, 70% were protein truncating (PT) and predicted to be definitively pathogenic.…”

“…12 With this advance, the Consortium for Radiologic Imaging Study of PKD (CRISP) reported a comprehensive survey of the spectrum of PKD1 and PKD2 mutations in 180 patients. 12 Among the putative deleterious PKD1 variants identified in 153 patients, 70% were protein truncating (PT) and predicted to be definitively pathogenic. By contrast, the clinical significance of the remaining nontruncating (NT) variants (i.e., small inframe deletion/insertion [IF indel], nonsynonymous missense, or atypical splice site variants) was less certain.…”

Whole-genome sequencing overcomes pseudogene homology to diagnose autosomal dominant polycystic kidney disease

“…1,5,6 This technique has a diagnostic rate of approximately 90% in well-phenotyped trial cohorts and 40-60% in the commercial reference laboratory. [7][8][9] The technique is labour intensive and thus expensive. More recently, targeted massively parallel sequencing (MPS) has been used to sequence PKD1 and PKD2.…”