Identification and Classification of Novel Genetic Variants: En Route to the Diagnosis of Primary Ciliary Dyskinesia

Abstract

Primary ciliary dyskinesia (PCD) is a disease caused by impaired function of motile cilia. PCD mainly affects the lungs and reproductive organs. Inheritance is autosomal recessive and X-linked. PCD patients have diverse clinical manifestations, thus making the establishment of proper diagnosis challenging. The utility of next-generation sequencing (NGS) technology for diagnostic purposes allows for better understanding of the PCD genetic background. However, identification of specific disease-causing variants is difficult. The main aim of this study was to create a unique guideline that will enable the standardization of the assessment of novel genetic variants within PCD-associated genes. The designed pipeline consists of three main steps: (1) sequencing, detection, and identification of genes/variants; (2) classification of variants according to their effect; and (3) variant characterization using in silico structural and functional analysis. The pipeline was validated through the analysis of the variants detected in a well-known PCD disease-causing gene (DNAI1) and the novel candidate gene (SPAG16). The application of this pipeline resulted in identification of potential disease-causing variants, as well as validation of the variants pathogenicity, through their analysis on transcriptional, translational, and posttranslational levels. The application of this pipeline leads to the confirmation of PCD diagnosis and enables a shift from candidate to PCD disease-causing gene.

Novel compound heterozygous CCDC40 mutations in a familial case of primary ciliary dyskinesia

“…Primary ciliary dyskinesia (PCD) (OMIM#244400) is a rare genetic disorder affecting between 1:15,000 and 1:30,000 individuals worldwide ( 1 , 2 ). Most PCD cases are inherited in an autosomal recessive manner, although rare cases have been reported to show X-linked inheritance ( 2 , 3 ).…”

“…Primary ciliary dyskinesia (PCD) (OMIM#244400) is a rare genetic disorder affecting between 1:15,000 and 1:30,000 individuals worldwide ( 1 , 2 ). Most PCD cases are inherited in an autosomal recessive manner, although rare cases have been reported to show X-linked inheritance ( 2 , 3 ). The disease is characterized by impaired function of motile cilia ( 4 ), and clinical manifestations include chronic or recurrent respiratory tract infections, situs inversus (SI), conductive hearing impairment, and infertility ( 5 ).…”

Perspectives for Primary Ciliary Dyskinesia

“…High-throughput DNA analysis technologies, which generate large amounts of data, must be analyzed in an appropriate manner to ensure that the identified variants are indeed causative for the disease. The article by Števanovic et al, proposes a unique pipeline that uses combination of data available from in silico databases, prediction tools and functional analyses to assess the pathogenic and clinical impact of a large number of genetic variants of unknown significance (VUS) identified in NGS sequencing [25]. The authors positively validated their pipeline by analyzing pathogenic impact of variants identified in both known and candidate PCD genes (DNAI1 and SPAG16, respectively), concluding that application of this approach could lead to a more reliable PCD diagnosis.…”