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Primary ciliary dyskinesia multigene NGS diagnostic testing in Cyprus

Citation

Yiallouros, Panayiotis et al. (2021), Primary ciliary dyskinesia multigene NGS diagnostic testing in Cyprus, Dryad, Dataset, https://doi.org/10.5061/dryad.c2fqz6177

Abstract

The dataset describes the genetic diagnosis in the national PCD cohort of Cyprus, an island with a high disease prevalence. Targeted next-generation sequencing (NGS) of 39 known PCD genes was carried out in samples from 48 patients of Greek-Cypriot and other ancestries. Molecular diagnosis was achived in 74% of the unrelated families tested (68% of Greek-Cypriot and 90% of non-Greek-Cypriot origin respectively). A total of 24 different mutations in 11 genes, 12 of which are novel were identified. These were categorized as nonsense (n= 9), splice-site (7), frameshift (n= 4), and missense (n= 3) mutations, and small deletions (n= 1). Homozygosity was more common in Greek-Cypriot than non-Greek-Cypriot patients (88% vs 46.2%, p =0.016). Four mutations (DNAH11:c.5095-2A>G, CFAP300:c.95_103delGCCGGCTCC, TTC25:c.716G>A, RSPH9: c.670+2T>C,) were found in 74% of the diagnosed Greek-Cypriot families, usually appearing in homozygosity and regional clusters. Patients with RSPH9 mutations demonstrated higher nasal nitric oxide production (57nL/min Vs 15 nL/min, p <0.001), higher FEV1 (-0.89 vs -2.37, p=0.018) and FVC (-1.00 vs -2.16, p=0.029) z-scores than the rest of the cohort. Targeted multigene-panel NGS diagnosis is an efficient single test for early diagnosis of PCD, providing insight to disease genetic epidemiology in isolated populations and improved patient stratification.

Methods

Diagnostic tests for PCD were performed as described previously (https://doi.org/10.1016/j.pupt.2017.10.010).  The performance of nNO measurement, HSVM and TEM evaluation were performed as described previously (Kouis et al., 2018). To discriminate abnormally low nNO, a cut-off of 77 nl/min was used (https://doi.org/10.1513/AnnalsATS.201305-110OC). HSVM analysis was performed and Ciliary Beat Frequency was quantified with the use of SAVA system. Ciliary Beat Pattern was determined with slow motion video playbacks (https://doi.org/10.1046/j.1365-2818.2003.01209.x). For classification of ciliary ultrastructure defects by TEM, the international consensus guideline for reporting transmission electron microscopy findings in the diagnosis of PCD (BEAT PCD TEM Criteria) was employed (Shoemark et al., 2020). Data on clinical manifestations were collected through a specific questionnaire and were routinely uploaded to the international PCD registry (DOI: 10.1183/13993003.00776-2015). Genetic screening of the known PCD-related genes was performed using a custom, targeted, 39-gene Next Generation Screening panel. Enrichment for the genomic regions of interest was performed using Agilent’s SureSelectQXT Target Enrichment System (Agilent Technologies, Santa Clara, CA, USA) following the manufacturer’s protocol. Libraries were sequenced on an Illumina MiSeq® platform following the manufacturer’s instructions. 

Usage Notes

No specific instructions are required. No missing values.

Please refer to the ReadMe files for the complete list of sequenced genes.

Funding

EU 7th Framework Program EC-GA - BESTCILIA, Award: 305404

EU 7th Framework Program EC-GA - BESTCILIA, Award: 305404