Open Access

Visual inspection reveals a novel pathogenic mutation in PKD1 missed by the variant caller in whole‑exome sequencing

  • Authors:
    • Bee Tee Koay
    • Mei Yee Chiow
    • Jamiila Ismail
    • Norfarhana Khairul Fahmy
    • Seow Yeing Yee
    • Norhazlin Mustafa
    • Masita Arip
    • Adiratna Mat Ripen
    • Saharuddin Bin Mohamad
  • View Affiliations

  • Published online on: October 24, 2022     https://doi.org/10.3892/mmr.2022.12882
  • Article Number: 365
  • Copyright: © Koay et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

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Abstract

Autosomal dominant polycystic kidney disease (ADPKD) is the most common type of inherited cystic kidney disease. The feasibility of whole‑exome sequencing (WES) to obtain molecular diagnosis of ADPKD is still in question as previous studies showed conflicting results. Utilizing WES on a patient with ADPKD, standard bioinformatics pipeline demonstrated no pathogenic variant in the genes of interest. By visualizing read alignments using the Integrative Genomics Viewer, a region with atypical alignment of numerous soft‑clipped reads at exon 45 of polycystin 1, transient receptor potential channel interacting (PKD1) gene was demonstrated. A total of four visual inspection steps were outlined to assess the origin of these soft‑clipped reads as strand bias during capture, poor mapping, sequencing error or DNA template contamination. Following assessment, the atypical alignment at PKD1 was hypothesized to be caused by an insertion/deletion mutation. Sanger sequencing confirmed the presence of a novel 20‑bp insertion in PKD1 (NM_001009944.3; c.12143_12144insTCC​CCG​CAG​TCT​TCC​CCG​CA; p.Val4048LeufsTer157), which introduced a premature stop codon and was predicted to be pathogenic. The present study demonstrated that WES could be utilized as a molecular diagnostic tool for ADPKD. Furthermore, visual inspection of read alignments was key in identifying the pathogenic variant. The proposed visual inspection steps may be incorporated into a typical WES data analysis workflow to improve the diagnostic yield.
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December-2022
Volume 26 Issue 6

Print ISSN: 1791-2997
Online ISSN:1791-3004

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Copy and paste a formatted citation
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Spandidos Publications style
Koay BT, Chiow MY, Ismail J, Fahmy NK, Yee SY, Mustafa N, Arip M, Ripen AM and Mohamad SB: Visual inspection reveals a novel pathogenic mutation in <em>PKD1</em> missed by the variant caller in whole‑exome sequencing. Mol Med Rep 26: 365, 2022.
APA
Koay, B.T., Chiow, M.Y., Ismail, J., Fahmy, N.K., Yee, S.Y., Mustafa, N. ... Mohamad, S.B. (2022). Visual inspection reveals a novel pathogenic mutation in <em>PKD1</em> missed by the variant caller in whole‑exome sequencing. Molecular Medicine Reports, 26, 365. https://doi.org/10.3892/mmr.2022.12882
MLA
Koay, B. T., Chiow, M. Y., Ismail, J., Fahmy, N. K., Yee, S. Y., Mustafa, N., Arip, M., Ripen, A. M., Mohamad, S. B."Visual inspection reveals a novel pathogenic mutation in <em>PKD1</em> missed by the variant caller in whole‑exome sequencing". Molecular Medicine Reports 26.6 (2022): 365.
Chicago
Koay, B. T., Chiow, M. Y., Ismail, J., Fahmy, N. K., Yee, S. Y., Mustafa, N., Arip, M., Ripen, A. M., Mohamad, S. B."Visual inspection reveals a novel pathogenic mutation in <em>PKD1</em> missed by the variant caller in whole‑exome sequencing". Molecular Medicine Reports 26, no. 6 (2022): 365. https://doi.org/10.3892/mmr.2022.12882