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RNA sequencing and target long-read sequencing reveal an intronic transposon insertion causing aberrant splicing
http://hdl.handle.net/10271/0002000464
http://hdl.handle.net/10271/0002000464752fbfc2-54d7-4b3e-8bca-15de97b89b85
| 名前 / ファイル | ライセンス | アクション |
|---|---|---|
論文本文 (5.3 MB)
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| Item type | 共通アイテムタイプ / Common item types(1) | |||||||||||
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| 公開日 | 2025-08-21 | |||||||||||
| タイトル | ||||||||||||
| タイトル | RNA sequencing and target long-read sequencing reveal an intronic transposon insertion causing aberrant splicing | |||||||||||
| 言語 | ||||||||||||
| 言語 | eng | |||||||||||
| キーワード | ||||||||||||
| 主題 | PCS/MVA syndrome | |||||||||||
| キーワード | ||||||||||||
| 主題 | long-read sequencing | |||||||||||
| キーワード | ||||||||||||
| 主題 | RNA sequencing | |||||||||||
| その他のタイトル | ||||||||||||
| その他のタイトル | RNAシーケンスとターゲットロングリードシーケンスによるスプライシング異常の原因となるイントロンでのトランスポゾン挿入の同定 | |||||||||||
| 資源タイプ | ||||||||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_db06 | |||||||||||
| 資源タイプ | doctoral thesis | |||||||||||
| アクセス権 | ||||||||||||
| アクセス権 | open access | |||||||||||
| アクセス権URI | http://purl.org/coar/access_right/c_abf2 | |||||||||||
| 著者 |
川上, 領太
× 川上, 領太
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| 書誌情報 |
en : Journal of Human Genetics 巻 69, 号 2, p. 91-99, 発行日 2024-02 |
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| 出版者 | ||||||||||||
| 出版者 | Springer Nature | |||||||||||
| 出版者 | ||||||||||||
| 出版者 | 日本人類遺伝学会 = The Japan Society of Human Genetics | |||||||||||
| 権利 | ||||||||||||
| 権利情報 | This version of the article has been accepted for publication, after peer review (when applicable) and is subject to Springer Nature’s AM terms of use, but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at: https://doi.org/10.1038/s10038-023-01211-8 | |||||||||||
| 抄録 | ||||||||||||
| 内容記述タイプ | Abstract | |||||||||||
| 内容記述 | More than half of cases with suspected genetic disorders remain unsolved by genetic analysis using short-read sequencing such as exome sequencing (ES) and genome sequencing (GS). RNA sequencing (RNA-seq) and long-read sequencing (LRS) are useful for interpretation of candidate variants and detection of structural variants containing repeat sequences, respectively. Recently, adaptive sampling on nanopore sequencers enables target LRS more easily. Here, we present a Japanese girl with premature chromatid separation (PCS)/mosaic variegated aneuploidy (MVA) syndrome. ES detected a known pathogenic maternal heterozygous variant (c.1402-5A>G) in intron 10 of BUB1B (NM_001211.6), a known responsive gene for PCS/MVA syndrome with autosomal recessive inheritance. Minigene splicing assay revealed that almost all transcripts from the c.1402-5G allele have mis-splicing with 4-bp insertion. GS could not detect another pathogenic variant, while RNA-seq revealed abnormal reads in intron 2. To extensively explore variants in intron 2, we performed adaptive sampling and identified a paternal 3.0 kb insertion. Consensus sequence of 16 reads spanning the insertion showed that the insertion consists of Alu and SVA elements. Realignment of RNA-seq reads to the new reference sequence containing the insertion revealed that 16 reads have 5’splice site within the insertion and 3’ splice site at exon 3, demonstrating causal relationship between the insertion and aberrant splicing. In addition, immunoblotting showed severely diminished BUB1B protein level in patient derived cells. These data suggest that detection of transcriptomic abnormalities by RNA-seq can be a clue for identifying pathogenic variants, and determination of insert sequences is one of merits of LRS. | |||||||||||
| 学位名 | ||||||||||||
| 学位名 | 博士（医学） | |||||||||||
| 学位の区分 | ||||||||||||
| 内容記述 | doctoral | |||||||||||
| 学位の分野 | ||||||||||||
| 内容記述 | 医学系研究科 | |||||||||||
| 学位授与機関 | ||||||||||||
| 学位授与機関名 | 浜松医科大学 | |||||||||||
| 学位授与機関名 | Hamamatsu University School of Medicine | |||||||||||
| 学位授与年月日 | ||||||||||||
| 学位授与年月日 | 2024-09-20 | |||||||||||
| 学位授与番号 | ||||||||||||
| 学位授与番号 | 甲第993号 | |||||||||||
| PISSN | ||||||||||||
| 収録物識別子 | 1434-5161 | |||||||||||
| EISSN | ||||||||||||
| 収録物識別子 | 1435-232X | |||||||||||
| NII書誌ID (NCID) | ||||||||||||
| 収録物識別子 | AA11206160 | |||||||||||
| PubMed番号 (PMID) | ||||||||||||
| 関連識別子 | 38102195 | |||||||||||
| 医中誌論文ID (ICHUSHI) | ||||||||||||
| 関連識別子 | 2025095065 | |||||||||||
| 出版社DOI | ||||||||||||
| 関連識別子 | https://doi.org/10.1038/s10038-023-01211-8 | |||||||||||
| 学位論文要旨/本文へのリンク | ||||||||||||
| 関連識別子 | http://hdl.handle.net/10271/0002000246 | |||||||||||
| 関連名称 | 学位論文要旨 | |||||||||||
| 出版タイプ | ||||||||||||
| 出版タイプ | AM | |||||||||||
| 出版タイプResource | http://purl.org/coar/version/c_ab4af688f83e57aa | |||||||||||
