Whole-Exome Sequencing and Targeted Copy Number Analysis in Primary Ciliary Dyskinesia

G3 (Bethesda). 2015 Jul 2;5(8):1775-81. doi: 10.1534/g3.115.019851.


Primary ciliary dyskinesia (PCD) is an autosomal-recessive disorder resulting from loss of normal ciliary function. Symptoms include neonatal respiratory distress, chronic sinusitis, bronchiectasis, situs inversus, and infertility. Clinical features may be subtle and highly variable, making the diagnosis of PCD challenging. The diagnosis can be confirmed with ciliary ultrastructure analysis and/or molecular genetic testing of 32 PCD-associated genes. However, because of this genetic heterogeneity, comprehensive molecular genetic testing is not considered the standard of care, and the most efficient molecular approach has yet to be elucidated. Here, we propose a cost-effective and time-efficient molecular genetic algorithm to solve cases of PCD. We conducted targeted copy number variation (CNV) analysis and/or whole-exome sequencing on 20 families (22 patients) from a subset of 45 families (52 patients) with a clinical diagnosis of PCD who did not have a molecular genetic diagnosis after Sanger sequencing of 12 PCD-associated genes. This combined molecular genetic approach led to the identification of 4 of 20 (20%) families with clinically significant CNVs and 7 of 20 (35%) families with biallelic pathogenic mutations in recently identified PCD genes, resulting in an increased molecular genetic diagnostic rate of 55% (11/20). In patients with a clinical diagnosis of PCD, whole-exome sequencing followed by targeted CNV analysis results in an overall molecular genetic yield of 76% (34/45).

Keywords: copy number variation; diagnostic testing; primary ciliary dyskinesia; whole-exome sequencing.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Adolescent
  • Adult
  • Algorithms
  • Axonemal Dyneins / genetics
  • Child
  • Child, Preschool
  • Ciliary Motility Disorders / diagnosis
  • Ciliary Motility Disorders / genetics*
  • Codon, Nonsense
  • Cytoskeletal Proteins
  • DNA Copy Number Variations*
  • Exome / genetics
  • Female
  • Frameshift Mutation
  • Genome, Human
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Infant
  • Male
  • Microtubule-Associated Proteins / genetics
  • Nerve Tissue Proteins / genetics
  • Nuclear Proteins / genetics
  • Sequence Analysis, DNA


  • Codon, Nonsense
  • Cytoskeletal Proteins
  • DNAAF3 protein, human
  • DNAAF4 protein, human
  • Microtubule-Associated Proteins
  • Nerve Tissue Proteins
  • Nuclear Proteins
  • Axonemal Dyneins

Supplementary concepts

  • Ciliary Dyskinesia, Primary, 12