Molecular Inversion Probe-Based Sequencing of <i>USH2A</i> Exons and Splice Sites as a Cost-Effective Screening Tool in USH2 and arRP Cases

A substantial proportion of subjects with autosomal recessive retinitis pigmentosa (arRP) or Usher syndrome type II (USH2) lacks a genetic diagnosis due to incomplete <i>USH2A</i> screening in the early days of genetic testing. These cases lack eligibility for optimal genetic counseling...

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Bibliographic Details
Main Authors: Janine Reurink, Adrian Dockery, Dominika Oziębło, G. Jane Farrar, Monika Ołdak, Jacoline B. ten Brink, Arthur A. Bergen, Tuula Rinne, Helger G. Yntema, Ronald J. E. Pennings, L. Ingeborgh van den Born, Marco Aben, Jaap Oostrik, Hanka Venselaar, Astrid S. Plomp, M. Imran Khan, Erwin van Wijk, Frans P. M. Cremers, Susanne Roosing, Hannie Kremer
Format: Article
Language:English
Published: MDPI AG 2021-06-01
Series:International Journal of Molecular Sciences
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Online Access:https://www.mdpi.com/1422-0067/22/12/6419
Description
Summary:A substantial proportion of subjects with autosomal recessive retinitis pigmentosa (arRP) or Usher syndrome type II (USH2) lacks a genetic diagnosis due to incomplete <i>USH2A</i> screening in the early days of genetic testing. These cases lack eligibility for optimal genetic counseling and future therapy. <i>USH2A</i> defects are the most frequent cause of USH2 and are also causative in individuals with arRP. Therefore, <i>USH2A</i> is an important target for genetic screening. The aim of this study was to assess unscreened or incompletely screened and unexplained USH2 and arRP cases for (likely) pathogenic <i>USH2A</i> variants. Molecular inversion probe (MIP)-based sequencing was performed for the <i>USH2A</i> exons and their flanking regions, as well as published deep-intronic variants. This was done to identify single nucleotide variants (SNVs) and copy number variants (CNVs) in 29 unscreened or partially pre-screened USH2 and 11 partially pre-screened arRP subjects. In 29 out of these 40 cases, two (likely) pathogenic variants were successfully identified. Four of the identified SNVs and one CNV were novel. One previously identified synonymous variant was demonstrated to affect pre-mRNA splicing. In conclusion, genetic diagnoses were obtained for a majority of cases, which confirms that MIP-based sequencing is an effective screening tool for <i>USH2A</i>. Seven unexplained cases were selected for future analysis with whole genome sequencing.
ISSN:1661-6596
1422-0067