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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Related Experiment Video

Updated: Sep 12, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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Noncoding DNA Variants Increase the Genetic Diagnostic Yield in Primary Ciliary Dyskinesia.

Lizi Briggs1, Cátia Brandão1, Andrew Fleming1

  • 1Clinical Genetics and Genomics Laboratory.

American Journal of Respiratory and Critical Care Medicine
|August 4, 2025
PubMed
Summary

Investigating non-coding regions significantly improves genetic diagnosis for primary ciliary dyskinesia (PCD). End-to-end gene sequencing identifies pathogenic variants missed by standard testing, aiding in diagnosing this rare respiratory disorder.

Keywords:
ciliopathygenetic testingnoncoding genomeprimary ciliary dyskinesia

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Area of Science:

  • Genetics
  • Respiratory Medicine
  • Molecular Biology

Background:

  • Primary ciliary dyskinesia (PCD) is a rare genetic respiratory disorder affecting motile cilia.
  • Current genetic testing often focuses on coding regions, leaving many patients without a complete diagnosis.
  • Pathogenic variants in over 50 genes are known to cause PCD.

Purpose of the Study:

  • To evaluate the diagnostic yield of genetic testing in 497 patients with suspected PCD.
  • To determine the increased diagnostic yield from investigating non-coding DNA regions in 42 patients with incomplete genetic diagnoses.
  • To identify novel pathogenic variants in the non-coding regions of PCD genes.

Main Methods:

  • Performed end-to-end next-generation sequencing of coding and non-coding regions for 17 PCD genes.
  • Utilized in silico tools to predict splice effects of intronic variants.
  • Confirmed predicted splice effects using RNA from nasal epithelium.

Main Results:

  • Routine genetic testing achieved a complete diagnosis in 46.8% of patients.
  • 17.3% of patients had an incomplete genetic diagnosis.
  • End-to-end sequencing identified novel pathogenic non-coding variants in 38.1% of patients with incomplete diagnoses, including three recurrent deep-intronic variants.

Conclusions:

  • End-to-end gene sequencing enhances the diagnostic yield for PCD.
  • Non-coding variants affecting splicing are a significant source of pathogenic variation in PCD.
  • This study highlights the clinical value of comprehensive gene or genome sequencing for PCD diagnosis.