An effective combination of sanger and next generation sequencing in diagnostics of primary ciliary dyskinesia

Djakow, Jana; Kramná, Lenka; Dušátková, Lenka; Uhlı́k, Jir̆ı́; Pursiheimo, Juha-Pekka; Svobodová, Tamara; Pohunek, Petr; Cinek, Ondřej

doi:10.1002/ppul.23261

Cited by 22 publications

(25 citation statements)

References 39 publications

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“…This was equivalent between patients with and without situs inversus and without any prior TEM, HSVM or nitric oxide screening; however, this cohort largely displays severe respiratory symptoms suggestive for PCD. This yield is comparable to the output of other studies, where causative mutations could be identified in 70 to 80% of PCD patients . Genetic testing has therefore proved to be a highly successful single test for PCD diagnosis in Egypt.…”

Section: Discussionsupporting

confidence: 70%

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Clinical and genetic spectrum in 33 Egyptian families with suspected primary ciliary dyskinesia

et al. 2019

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Primary ciliary dyskinesia (PCD) is a rare genetic disorder of motile cilia dysfunction generally inherited as an autosomal recessive disease. Genetic testing is increasingly considered an early step in the PCD diagnostic workflow. We used targeted panel next‐generation sequencing (NGS) for genetic screening of 33 Egyptian families with clinically highly suspected PCD. All variants prioritized were Sanger confirmed in the affected individuals and correctly segregated within the family. Targeted NGS yielded a high diagnostic output (70%) with biallelic mutations identified in known PCD genes. Mutations were identified in 13 genes overall, with CCDC40 and CCDC39 the most frequently mutated genes among Egyptian patients. Most identified mutations were predicted null effect variants (79%) and not reported before (85%). This study reveals that the genetic landscape of PCD among Egyptians is highly heterogeneous, indicating that a targeted NGS approach covering multiple genes will provide a superior diagnostic yield compared to Sanger sequencing for genetic diagnosis. The high diagnostic output achieved here highlights the potential of placing genetic testing early within the diagnostic workflow for PCD, in particular in developing countries where other diagnostic tests can be less available.

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Section: Discussionsupporting

confidence: 70%

“…This yield is comparable to the output of other studies, where causative mutations could be identified in 70 to 80% of PCD patients. [22][23][24][25] Genetic testing has therefore proved to be a highly successful single test for PCD diagnosis in Egypt.…”

Section: Discussionmentioning

confidence: 99%

Clinical and genetic spectrum in 33 Egyptian families with suspected primary ciliary dyskinesia

et al. 2019

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“…The extensive genetic heterogeneity in PCD makes NGS approaches also attractive for use in the diagnostic setting, as it offers parallel sequencing of multiple genes or of the entire exome. The diagnostic yield of targeted NGS panels used in Europe and the United States currently varies between 43% and 76% (Boaretto et al., ; Djakow et al., ; Marshall et al., ). This means that genetic testing cannot yet provide enough certainty to be used as the sole test for PCD.…”

Section: Introductionmentioning

confidence: 99%

Diagnostic yield of a targeted gene panel in primary ciliary dyskinesia patients

et al. 2018

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We aimed to determine the diagnostic yield of a targeted-exome panel in a cohort of 74 Dutch primary ciliary dyskinesia (PCD) patients. The panel consisted of 26 PCD-related and 284 candidate genes. To prioritize PCD candidate genes, we investigated the transcriptome of human airway cells of 12 healthy volunteers during in vitro ciliogenesis and hypothesized that PCD-related genes show significant upregulation. We compared gene expression in epithelial precursor cells grown as collagen monolayer and ciliated cells grown in suspension by RNA sequencing. All genes reported as PCD causative, except NME8, showed significant upregulation during in vitro ciliogenesis. We observed 67.6% diagnostic yield when testing the targeted-exome panel in our cohort. There was relatively high percentage of DNAI and HYDIN mutations compared to other countries. The latter may be due to our solution for the problem of the confounding HYDIN2 pseudogene. Candidate genes included two recently published PCD-related genes DNAJB13 and PIH1D3; identification of the latter was a direct result of this study. In conclusion, we demonstrate 67.6% diagnostic yield by targeted exome sequencing in a Dutch PCD population and present a highly sensitive and moderately specific approach for identification of PCD-related genes, based on significant upregulation during in vitro ciliogenesis.

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“…Investigators from the Czech Republic reported on a method utilizing an initial step of Sanger sequencing a small panel of genes for variants commonly found in the Czech population, followed by screening of a broader panel employing next-generation sequencing (NGS). 63 This approach provided timely, accurate, and cost-effective results, and identified a causative variant in two-thirds of tested patients. This may serve as a model for developing similar approaches, accounting for known population prevalence.…”

Section: Consensus Panel Recommendations and Expert Opinion Is Criticmentioning

confidence: 99%

“…Given the amount of genetic heterogeneity, testing for genetic causes of PCD has proven to be challenging. Investigators from the Czech Republic reported on a method utilizing an initial step of Sanger sequencing a small panel of genes for variants commonly found in the Czech population, followed by screening of a broader panel employing next‐generation sequencing (NGS) . This approach provided timely, accurate, and cost‐effective results, and identified a causative variant in two‐thirds of tested patients.…”

Section: Rare Lung Diseasementioning

confidence: 99%

Pediatric Pulmonologyyear in review 2016: Part 1

et al. 2017

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Our journal covers a broad range of research and scholarly topics related to children's respiratory disorders. For updated perspectives on the rapidly expanding knowledge in our field, we will summarize the past year's publications in our major topic areas, as well as selected publications in these areas from the core clinical journal literature outside our own pages. The current review covers articles on neonatal lung disease, pulmonary physiology, and respiratory infection.Word count: 71 3

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An effective combination of sanger and next generation sequencing in diagnostics of primary ciliary dyskinesia

Cited by 22 publications

References 39 publications

Clinical and genetic spectrum in 33 Egyptian families with suspected primary ciliary dyskinesia

Clinical and genetic spectrum in 33 Egyptian families with suspected primary ciliary dyskinesia

Diagnostic yield of a targeted gene panel in primary ciliary dyskinesia patients

Pediatric Pulmonologyyear in review 2016: Part 1

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