Targeted long-read nanopore sequencing as a complementary approach for detecting STRC variants and distinguishing the STRCP1 pseudogene.
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| Název: | Targeted long-read nanopore sequencing as a complementary approach for detecting STRC variants and distinguishing the STRCP1 pseudogene. |
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| Autoři: | Moteki H; Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Nagano, Japan. moteki@shinshu-u.ac.jp.; Department of Otolaryngology, Aizawa Hospital, Matsumoto, Japan. moteki@shinshu-u.ac.jp., Nishio SY; Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Nagano, Japan., Usami SI; Department of Hearing Implant Sciences, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, 390-8621, Nagano, Japan. |
| Zdroj: | Scientific reports [Sci Rep] 2025 Dec 22; Vol. 15 (1), pp. 44261. Date of Electronic Publication: 2025 Dec 22. |
| Způsob vydávání: | Journal Article |
| Jazyk: | English |
| Informace o časopise: | Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: London : Nature Publishing Group, copyright 2011- |
| Výrazy ze slovníku MeSH: | Pseudogenes* , Nanopore Sequencing*/methods , Hearing Loss, Sensorineural*/genetics, Humans ; Polymorphism, Single Nucleotide ; Male ; INDEL Mutation ; Female ; DNA Copy Number Variations ; High-Throughput Nucleotide Sequencing ; Intercellular Signaling Peptides and Proteins |
| Abstrakt: | The stereocilin (STRC) gene is a significant contributor to mild-to-moderate sensorineural hearing loss (SNHL), particularly in cases of biallelic STRC deletions and copy number alterations. Although pathogenic single nucleotide variants (SNVs) or small insertion-deletions (indels) have been investigated across the coding region of STRC, the pseudogene STRCP1, which shares 98% homology with the STRC gene, makes interpreting sequence data from this region challenging. To detect missing SNVs, targeted long-read sequencing was conducted using the nanopore MinION platform coupled with long-range polymerase chain reaction (PCR) enrichment on individuals exhibiting heterozygous STRC deletions and associated phenotypes. Sequencing results were obtained from 149 DNA samples. The median number of reads and depth of coverage were 4,088 and 2,780, respectively. The average read length of 20.76 kbp corresponded to that of a long-range PCR product, indicating precise analysis using MinION. Forty-three individuals carrying SNVs or small indels and 27 variants were identified. Thirteen were previously reported as hearing loss-causing variants and 14 were novel variants. Long-read sequencing technology enables precise detection of pathogenic variants in complex genomic regions, such as STRC, where conventional methods face challenges owing to pseudogene interference. Therefore, this approach is a valuable complement to conventional methods for resolving unresolved SNHL. This study demonstrates the utility of targeted long-read sequencing as a complementary method to short-read NGS for resolving complex regions such as STRC. The combination with long-range PCR enabled precise enrichment and improved resolution in SNV detection. (© 2025. The Author(s).) |
| Competing Interests: | Declaration. Competing interests: The authors declare no competing interests. Ethics approval and consent to participate: All procedures were approved by the Shinshu University Ethical Committee and the ethical committees of the other participating institutions. Informed consent was obtained from all participants or the parents of the proband for participation in this study, which was approved by the ethics committee of each institution. |
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| Contributed Indexing: | Keywords: STRC; Hearing loss; Long-read sequencing |
| Substance Nomenclature: | 0 (STRC protein, human) 0 (Intercellular Signaling Peptides and Proteins) |
| Entry Date(s): | Date Created: 20251222 Date Completed: 20251222 Latest Revision: 20251225 |
| Update Code: | 20251225 |
| PubMed Central ID: | PMC12722244 |
| DOI: | 10.1038/s41598-025-27816-x |
| PMID: | 41430084 |
| Databáze: | MEDLINE |
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Nájsť tento článok vo Web of Science | Abstrakt: | The stereocilin (STRC) gene is a significant contributor to mild-to-moderate sensorineural hearing loss (SNHL), particularly in cases of biallelic STRC deletions and copy number alterations. Although pathogenic single nucleotide variants (SNVs) or small insertion-deletions (indels) have been investigated across the coding region of STRC, the pseudogene STRCP1, which shares 98% homology with the STRC gene, makes interpreting sequence data from this region challenging. To detect missing SNVs, targeted long-read sequencing was conducted using the nanopore MinION platform coupled with long-range polymerase chain reaction (PCR) enrichment on individuals exhibiting heterozygous STRC deletions and associated phenotypes. Sequencing results were obtained from 149 DNA samples. The median number of reads and depth of coverage were 4,088 and 2,780, respectively. The average read length of 20.76 kbp corresponded to that of a long-range PCR product, indicating precise analysis using MinION. Forty-three individuals carrying SNVs or small indels and 27 variants were identified. Thirteen were previously reported as hearing loss-causing variants and 14 were novel variants. Long-read sequencing technology enables precise detection of pathogenic variants in complex genomic regions, such as STRC, where conventional methods face challenges owing to pseudogene interference. Therefore, this approach is a valuable complement to conventional methods for resolving unresolved SNHL. This study demonstrates the utility of targeted long-read sequencing as a complementary method to short-read NGS for resolving complex regions such as STRC. The combination with long-range PCR enabled precise enrichment and improved resolution in SNV detection.<br /> (© 2025. The Author(s).) |
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| ISSN: | 2045-2322 |
| DOI: | 10.1038/s41598-025-27816-x |