Analyses of 1236 genotyped primary ciliary dyskinesia individuals identify regional clusters of distinct DNA variants and significant genotype-phenotype correlations

Abstract

Background: Primary ciliary dyskinesia (PCD) represents a group of rare hereditary disorders characterised by deficient ciliary airway clearance that can be associated with laterality defects. We aimed to describe the underlying gene defects, geographical differences in genotypes and their relationship to diagnostic findings and clinical phenotypes.

Methods: Genetic variants and clinical findings (age, sex, body mass index, laterality defects, forced expiratory volume in 1 s (FEV₁)) were collected from 19 countries using the European Reference Network's ERN-LUNG international PCD Registry. Genetic data were evaluated according to American College of Medical Genetics and Genomics guidelines. We assessed regional distribution of implicated genes and genetic variants as well as genotype correlations with laterality defects and FEV₁.

Results: The study included 1236 individuals carrying 908 distinct pathogenic DNA variants in 46 PCD genes. We found considerable variation in the distribution of PCD genotypes across countries due to the presence of distinct founder variants. The prevalence of PCD genotypes associated with pathognomonic ultrastructural defects (mean 72%, range 47-100%) and laterality defects (mean 42%, range 28-69%) varied widely among countries. The prevalence of laterality defects was significantly lower in PCD individuals without pathognomonic ciliary ultrastructure defects (18%). The PCD cohort had a reduced median FEV₁ z-score (-1.66). Median FEV₁ z-scores were significantly lower in CCNO (-3.26), CCDC39 (-2.49) and CCDC40 (-2.96) variant groups, while the FEV₁ z-score reductions were significantly milder in DNAH11 (-0.83) and ODAD1 (-0.85) variant groups compared to the whole PCD cohort.

Conclusion: This unprecedented multinational dataset of DNA variants and information on their distribution across countries facilitates interpretation of the genetic epidemiology of PCD and indicates that the genetic variant can predict diagnostic and phenotypic features such as the course of lung function.

Outline of the study. ERN: European Reference Network; PCD: primary ciliary dyskinesia; ACMG: American College of Medical Genetics and Genomics; FEV₁: forced expiratory volume in 1 s. **: p≤0.01; ****: p≤0.0001.

FIGURE 1

The regional distribution and number of individuals with confirmed pathogenic variants in primary ciliary dyskinesia-associated genes among 34 centres from 19 different countries.

FIGURE 2

The most frequent pathogenic genetic variants in selected primary ciliary dyskinesia genes and their regional distribution. The most common variants in DNAH5, CCDC40, DNAI1, SPAG1 and CCNO show regional clusters. a) The most common DNAH5 variant c.10815del (×46) is prevalent in northern Europe. b) The most common CCDC40 variant c.248del (×69) is also frequently reported in the northern parts of Europe. c) The most common DNAI1 variant c.48+2dup (×60) predominantly occurs in northern Europe and neighbouring countries. d) The most common SPAG1 variant c.2014C>T (×56) shows a dominant regional distribution in the Slavic countries Poland, Czech Republic and Slovakia. e) In CCNO, there are two frequent genetic variants: c.248_252dup (×18) mainly occurs in Turkey, whereas c.258_262dup (×16) is mainly reported in Israel. NA: not available.

FIGURE 3

The most frequent pathogenic gene variants associated with primary ciliary dyskinesia per country. There are clear regional differences between countries. The total absolute and relative frequency of the most frequent variant per country is shown in brackets. The variant c.2014C>T in SPAG1 (mint green) is the most frequently reported variant in Poland (24 out of 268 variants, 0.0896), the Czech Republic (12 out of 46 variants, 0.2609) and Slovakia (10 out of 16 variants, 0.625). The variant c.742G>A in ODAD1 (pale pink) prevails in the Netherlands. The variant c.248_252dup in CCNO (yellow) is the most frequently detected variant in Turkey and c.248del in CCDC40 (dark green) is the most frequently detected variant in Denmark (17 out of 182 variants, 0.0934), Norway (9 out of 80 variants, 0.1125) and Belgium (5 out of 64 variants, 0.0781). Despite the overall high involvement of DNAH5 (figure 1), none of its variants was identified as the most frequent in any of the countries. Argentina and Brazil are not shown (no most frequent genetic variant).

FIGURE 4

Prevalence of laterality defects per predicted ciliary ultrastructure and country. The prevalence of laterality defects is 42% in the total study cohort (n=519 individuals with laterality defects). There is a significant difference between the groups stratified according to the predicted effect of genetic variants on ciliary ultrastructure. In the group of 894 individuals with genetic variants associated with pathognomonic ciliary ultrastructure defects detectable by transmission electron microscopy, 51% of individuals (n=457) have laterality defects. In contrast, in the group of individuals with genetic variants not associated with defective ciliary ultrastructure hallmark, only 18% of individuals (n=55) have laterality defects (p<0.0001). The prevalence of laterality defects varies widely among the participating countries and ranges from 28% to 69%. It is lowest in Turkey (28%), the Netherlands (31%), Germany (37%), Spain (39%) and Israel (40%).

FIGURE 5

Median forced expiratory volume in 1 s (FEV₁) z-scores of the whole primary ciliary dyskinesia (PCD) cohort and distinct PCD groups. a) The median FEV₁ z-score of the overall PCD cohort is −1.66 (interquartile range (IQR) −2.75– −0.752). Individuals with CCNO variants (n=25) show a significantly lower median FEV₁ z-score (−3.26, IQR −5.04– −2.13, p<0.0001) compared to the rest of the cohort. Individuals with DNA variants in CCDC39 (n=64) and CCDC40 (n=101) associated with microtubular disorganisation and inner dynein arm defects exhibit median FEV₁ z-scores significantly lower than the rest of the cohort (CCDC39: −2.49, IQR −3.28– −1.37, p<0.01; CCDC40: −2.96, IQR −3.77– −1.86, p<0.00001). The group of individuals with DNAH11 (n=119) and ODAD1 variants (n=34) show significantly higher median FEV₁ z-scores compared to the rest of the cohort (DNAH11: −0.831, IQR −1.57– −0.0984, p<0.0001; ODAD1 −0.850, IQR −1.57– −0.0984, p<0.01). Significant differences between distinct gene groups and the rest of the cohort are marked with asterisks. p≤0.05 was considered significant. **: p≤0.01; ****: p≤0.0001. b) The study cohort was divided into consecutive 5-year age groups to analyse age-dependence of FEV₁ z-scores. 528 PCD individuals have FEV₁ data represented in more than one age bin. Groups of older PCD individuals have increasingly lower FEV₁ z-scores (grey bars). The groups of individuals with CCNO, CCDC39 and CCDC40 variants have lower FEV₁ z-scores, while individuals with DNAH11 and ODAD1 variants have higher FEV₁ z-scores in most age bins compared to the total cohort. However, the median FEV₁ z-scores of the DNAH11 and ODAD1 variant group of individuals aged >60 or >30–35 years, respectively, show similarly low values as the total PCD cohort.