Diagnostic yield of a targeted gene panel in primary ciliary dyskinesia patients

• Published in: Human mutation Vol. 39; no. 5; pp. 653 - 665
• Main Authors: Paff, Tamara, Kooi, Irsan E., Moutaouakil, Youssef, Riesebos, Elise, Sistermans, Erik A., Daniels, Hans J. M. A., Weiss, Janneke M. M., Niessen, Hans H. W. M., Haarman, Eric G., Pals, Gerard, Micha, Dimitra
• Format: Journal Article
• Language: English
• Published: United States Hindawi Limited 01-05-2018
• Subjects: Adult; Alleles; ciliogenesis; Collagen; Exome - genetics; Gene expression; Gene Expression Regulation; Humans; Kartagener Syndrome - diagnosis; Kartagener Syndrome - genetics; Mutation; Mutation - genetics; Primary ciliary dyskinesia; Respiratory tract; Ribonucleic acid; RNA; RNA sequencing; Sequence Analysis, RNA; targeted exome sequencing; RNA sequencing; ciliogenesis; primary ciliary dyskinesia; targeted exome sequencing
• ISSN: 1059-7794; 1098-1004
• DOI: 10.1002/humu.23403

We aimed to determine the diagnostic yield of a targeted‐exome panel in a cohort of 74 Dutch primary ciliary dyskinesia (PCD) patients. The panel consisted of 26 PCD‐related and 284 candidate genes. To prioritize PCD candidate genes, we investigated the transcriptome of human airway cells of 12 healthy volunteers during in vitro ciliogenesis and hypothesized that PCD‐related genes show significant upregulation. We compared gene expression in epithelial precursor cells grown as collagen monolayer and ciliated cells grown in suspension by RNA sequencing. All genes reported as PCD causative, except NME8, showed significant upregulation during in vitro ciliogenesis. We observed 67.6% diagnostic yield when testing the targeted‐exome panel in our cohort. There was relatively high percentage of DNAI and HYDIN mutations compared to other countries. The latter may be due to our solution for the problem of the confounding HYDIN2 pseudogene. Candidate genes included two recently published PCD‐related genes DNAJB13 and PIH1D3; identification of the latter was a direct result of this study. In conclusion, we demonstrate 67.6% diagnostic yield by targeted exome sequencing in a Dutch PCD population and present a highly sensitive and moderately specific approach for identification of PCD‐related genes, based on significant upregulation during in vitro ciliogenesis.
The diagnostic yield of a targeted‐exome panel, consisting of 26 known and 284 candidate genes, was determined in a Dutch cohort of 74 PCD patients. The candidate genes were prioritized based on significant upregulation during in vitro ciliogenesis. We determined 67.6% diagnostic yield. A high percentage of DNAI and HYDIN mutations was observed in relation to other countries, potentially owing to our proposed solution for filtering out interference of the HYDIN2 pseudogene in NGS analysis.