Whole genome sequencing in the diagnosis of primary ciliary dyskinesia

N Simon Thomas,Mary Carroll,Gabrielle Wheway,Janice Coles,David Hunt,Jane S Lucas,Claire L Jackson,Patricia Goggin,Regan Doherty,Ben Green,Jenny Lord,Woolf T Walker,Amanda Harris,Vito Mennella,James Thompson

doi:10.1186/s12920-021-01084-w

Abstract

BackgroundIt is estimated that 1–13% of cases of bronchiectasis in adults globally are attributable to primary ciliary dyskinesia (PCD) but many adult patients with bronchiectasis have not been investigated for PCD. PCD is a disorder caused by mutations in genes required for motile cilium structure or function, resulting in impaired mucociliary clearance. Symptoms appear in infancy but diagnosis is often late or missed, often due to the lack of a “gold standard” diagnostic tool and non-specific symptoms. Mutations in > 50 genes account for around 70% of cases, with additional genes, and non-coding, synonymous, missense changes or structural variants (SVs) in known genes presumed to account for the missing heritability.MethodsUK patients with no identified genetic confirmation for the cause of their PCD or bronchiectasis were eligible for whole genome sequencing (WGS) in the Genomics England Ltd 100,000 Genomes Project. 21 PCD probands and 52 non-cystic fibrosis (CF) bronchiectasis probands were recruited in Wessex Genome Medicine Centre (GMC). We carried out analysis of single nucleotide variants (SNVs) and SVs in all families recruited in Wessex GMC.Results16/21 probands in the PCD cohort received confirmed (n = 9), probable (n = 4) or possible (n = 3) diagnosis from WGS, although 13/16 of these could have been picked up by current standard of care gene panel testing. In the other cases, SVs were identified which were missed by panel testing. We identified variants in novel PCD candidate genes (IFT140 and PLK4) in 2 probands in the PCD cohort. 3/52 probands in the non-CF bronchiectasis cohort received a confirmed (n = 2) or possible (n = 1) diagnosis of PCD. We identified variants in novel PCD candidate genes (CFAP53 and CEP164) in 2 further probands in the non-CF bronchiectasis cohort.ConclusionsGenetic testing is an important component of diagnosing PCD, especially in cases of atypical disease history. WGS is effective in cases where prior gene panel testing has found no variants or only heterozygous variants. In these cases it may detect SVs and is a powerful tool for novel gene discovery.

Highlights

It is estimated that 1–13% of cases of bronchiectasis in adults globally are attributable to primary ciliary dyskinesia (PCD) but many adult patients with bronchiectasis have not been investigated for PCD
Results of Small nucleotide variant (SNV) analysis in PCD cohort Tier 1 or tier 2 variants were found in 12/21 patients
A diagnosis was possible in the 2 cases that had undergone prior testing because either additional cases were available in the literature or parental testing demonstrated that the variants were in trans; whole genome sequencing (WGS) did not identify any additional variants

Summary

Introduction

It is estimated that 1–13% of cases of bronchiectasis in adults globally are attributable to primary ciliary dyskinesia (PCD) but many adult patients with bronchiectasis have not been investigated for PCD. Symptoms appear in infancy but diagnosis is often late or missed, often due to the lack of a “gold standard” diagnostic tool and non-specific symptoms. Bronchiectasis is a disorder of persistent or recurrent bronchial infection, chronic cough, and purulent sputum production, associated with permanent airway dilatation. It is the end-point of various diseases and pathological mechanisms, and diagnosing bronchiectasis should be the starting point to finding the underlying cause. In most Western populations, genetic conditions including cystic fibrosis (CF), primary ciliary dyskinesia (PCD) and primary immunodeficiency disorders are common causes of bronchiectasis. The reasons for missed or late diagnoses are multi-factorial including no “gold standard” diagnostic tool, insufficient specialist diagnostic centres and clinicians’ lack of awareness about PCD [3]. Patients with dextrocardia, which is rare in the general population but affects 50% of people with PCD, are diagnosed earlier than those with normal organ situs [2]

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