An Efficient and Comprehensive Strategy for Genetic Diagnostics of Polycystic Kidney Disease

Eisenberger, Tobias; Decker, Christian; Hiersche, Milan; Hamann, Ruben C.; Decker, Eva L.; Neuber, Steffen; Frank, Valeska; Bolz, Hanno J.; Fehrenbach, Henry; Pape, Lars; Toenshoff, Burkhard; Mache, Christoph J.; Latta, Kay; Bergmann, Carsten

doi:10.1371/journal.pone.0116680

Cited by 68 publications

(63 citation statements)

References 37 publications

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“…11,12 As three of these exons fall outside of the pseudogene region, we attribute this lower sequencing depth to GC content rather than homology to the pseudogenes. Reduced coverage due to high GC content is likely due to PCR amplification bias during library creation and clonal amplification on the flowcell surface.…”

Section: Discussionmentioning

confidence: 99%

“…5,[10][11][12] An amplicon-based strategy using LR-PCR amplification of PKD1 and PKD2 exons, followed by MPS obtained a diagnostic rate of~60% in cohorts selected using only imaging criteria (ie, for whom a diseasecausing variant was not already known). 5,[10][11][12] These techniques are laborious and the PCR amplification process is error prone. Capturebased strategies have been trialled, to enrich for PKD1 and PKD2 exons, and in a small discovery cohort (n = 12) the diagnostic rate was 83%.…”

Section: Introductionmentioning

confidence: 99%

“…13 Furthermore, it is difficult to design short (65 nt) oligonucleotide capture probes that avoid selecting PKD1 pseudogenes. 11,12 Finally, the use of customdesigned capture probes requires pooling of samples to be cost effective, which may add significant delays in the clinical setting. PKD2 is a 68.0 kb gene in chromosome 4, comprising 15 exons.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2016

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Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic kidney disorder and is due to diseasecausing variants in PKD1 or PKD2. Strong genotype-phenotype correlation exists although diagnostic sequencing is not part of routine clinical practice. This is because PKD1 bears 97.7% sequence similarity with six pseudogenes, requiring laborious and error-prone long-range PCR and Sanger sequencing to overcome. We hypothesised that whole-genome sequencing (WGS) would be able to overcome the problem of this sequence homology, because of 150 bp, paired-end reads and avoidance of capture bias that arises from targeted sequencing. We prospectively recruited a cohort of 28 unique pedigrees with ADPKD phenotype. Standard DNA extraction, library preparation and WGS were performed using Illumina HiSeq X and variants were classified following standard guidelines. Molecular diagnosis was made in 24 patients (86%), with 100% variant confirmation by current gold standard of long-range PCR and Sanger sequencing. We demonstrated unique alignment of sequencing reads over the pseudogene-homologous region. In addition to identifying function-affecting single-nucleotide variants and indels, we identified single-and multi-exon deletions affecting PKD1 and PKD2, which would have been challenging to identify using exome sequencing. We report the first use of WGS to diagnose ADPKD. This method overcomes pseudogene homology, provides uniform coverage, detects all variant types in a single test and is less labour-intensive than current techniques. This technique is translatable to a diagnostic setting, allows clinicians to make better-informed management decisions and has implications for other disease groups that are challenged by regions of confounding sequence homology.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2016

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“…However, optimization of targeted sequence capture approaches or the methodological advantages of WGS now allow mutation analysis by NGS of even highly confounding loci such as PKD1 [30]. NGS approaches are nowadays the gold standard for genetic screening for ADPKD and should encompass a number of other genes besides the ones discussed above such as GANAB or HNF1β that were recently described to be mutated in a subset of patients with ADPKD [31].…”

Section: Autosomal Dominant Pkdmentioning

confidence: 99%

Early and Severe Polycystic Kidney Disease and Related Ciliopathies: An Emerging Field of Interest

Bergmann¹

2018

Nephron

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Early and severe forms of polycystic kidney disease (PKD) do already manifest during childhood or adolescence. They are characterized by enlarged kidneys and diminished renal function that prenatally may result in Potter’s oligohydramnios sequence. Genetically, various defects can mimic this phenotype. Most common are PKHD1 mutations that lead to autosomal recessive PKD (ARPKD). About the same number of children do carry mutations in the dominant autosomal dominant polycystic kidney disease (ADPKD) genes, PKD1 and less frequent PKD2, often arise de novo or may affect both disease alleles in a recessive mode. Mutations in DZIP1L have been recently described to result in an ARPKD-like phenotype. Likewise, mutations in several other cystogenes can phenocopy early and severe PKD. Early and reliable prenatal diagnosis for which there is a strong demand in ARPKD and related diseases is feasible only by genetics. A comprehensive knowledge of disease-causing genes is essential for the correct diagnosis and parental counselling. The increasing number of genes that need to be considered benefits from the advances of next generation sequencing and allows the simultaneous analysis of all genes of interest in a single test, which is now the mainstay for genetic diagnosis. Interpretation of data is challenging and requires expert knowledge in data handling, bioinformatics and clinical genetics.

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“…A further 1330 patients with a PKD phenotype (n=525) or a nephronopthisis (NPHP)-related complex ciliopathy (n=805) were analyzed by nextgeneration sequencing (NGS), mainly targeted multi-gene panel testing 16 . Thereby, we identified different homozygous protein truncating DZIP1L mutations (c.463C>T; (p.Gln155 * ) and c.1061_1062del; (p.Glu354Alafs * 39)) in two additional unrelated consanguineous pedigrees, B155 and B8031, with hallmarks of ARPKD (Fig.…”

Section: Dzip1l Is a New Arpkd Genementioning

confidence: 99%

Mutations in DZIP1L, which encodes a ciliary transition zone protein, cause autosomal recessive polycystic kidney disease

2017

Mechanisms of Development

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Author contributions LH, PJK, SYT, SV, and SR performed the zebrafish mutant and morphant analysis, protein interaction studies, localization experiments with human fibroblasts and validation of PC antibodies. WH supervised the protein interaction studies. EO, CK and DE performed the zebrafish morpholino analysis. MCRG, GK, VM and ADC performed the mouse analyses, and MCRG and GK performed the localization experiments with mouse cells. RT, PP and ACP performed the screen that identified the mouse mutant, and BW was involved in mapping and identifying the mouse mutation. GDW performed the superresolution microscopy experiments. MHL assisted with design and analysis of mouse kidney experiments. NOB, NH, VF, and SN performed the human mutation analysis. SN, VF, MH, HYG, EAO, FH, and CB carried out the WES data processing and analyses. SN, VF, EW, UV, HYG, KZ, FH, and CB recruited and clinically characterized the study subjects and collected samples. BH performed histologic evaluation of the data. SR, CW, and CB conceived the project, designed and supervised the experiments, analysed and interpreted the data, and wrote the manuscript. All authors reviewed the final manuscript. Competing financial interest statementThe authors declare that there are no competing financial interests. HHS Public AccessAuthor manuscript Nat Genet. Author manuscript; available in PMC 2018 January 01. AbstractAutosomal recessive polycystic kidney disease (ARPKD), usually considered to be a genetically homogeneous disease caused by mutations in PKHD1, has been associated with ciliary dysfunction. Here, we describe mutations in the DAZ interacting protein 1-like (DZIP1L) gene in patients with ARPKD, findings we have further validated by loss-of-function studies in mice and zebrafish. DZIP1L localizes to centrioles and at the distal end of basal bodies, and interacts with septin2, a protein implicated in maintenance of the periciliary diffusion barrier at the ciliary transition zone. Consistent with a defect in the diffusion barrier, we found that the ciliary membrane translocation of the PKD proteins, polycystin-1 and −2, is compromised in DZIP1L mutant cells. Together, these data provide the first conclusive evidence that ARPKD is not a homogeneous disorder, and establishes DZIP1L as a second gene involved in its pathogenesis.

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An Efficient and Comprehensive Strategy for Genetic Diagnostics of Polycystic Kidney Disease

Cited by 68 publications

References 37 publications

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

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

Early and Severe Polycystic Kidney Disease and Related Ciliopathies: An Emerging Field of Interest

Mutations in DZIP1L, which encodes a ciliary transition zone protein, cause autosomal recessive polycystic kidney disease

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