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dc.contributor.author | Mizuno, Kei | en |
dc.contributor.author | Akamatsu, Shusuke | en |
dc.contributor.author | Sumiyoshi, Takayuki | en |
dc.contributor.author | Wong, Jing Hao | en |
dc.contributor.author | Fujita, Masashi | en |
dc.contributor.author | Maejima, Kazuaki | en |
dc.contributor.author | Nakano, Kaoru | en |
dc.contributor.author | Ono, Atushi | en |
dc.contributor.author | Aikata, Hiroshi | en |
dc.contributor.author | Ueno, Masaki | en |
dc.contributor.author | Hayami, Shinya | en |
dc.contributor.author | Yamaue, Hiroki | en |
dc.contributor.author | Chayama, Kazuaki | en |
dc.contributor.author | Inoue, Takahiro | en |
dc.contributor.author | Ogawa, Osamu | en |
dc.contributor.author | Nakagawa, Hidewaki | en |
dc.contributor.author | Fujimoto, Akihiro | en |
dc.contributor.alternative | 水野, 桂 | ja |
dc.contributor.alternative | 赤松, 秀輔 | ja |
dc.contributor.alternative | 住吉, 崇幸 | ja |
dc.contributor.alternative | 藤田, 征志 | ja |
dc.contributor.alternative | 大野, 敦司 | ja |
dc.contributor.alternative | 相方, 浩 | ja |
dc.contributor.alternative | 上野, 昌樹 | ja |
dc.contributor.alternative | 速水, 晋也 | ja |
dc.contributor.alternative | 山上, 裕機 | ja |
dc.contributor.alternative | 茶山, 一彰 | ja |
dc.contributor.alternative | 井上, 貴博 | ja |
dc.contributor.alternative | 小川, 修 | ja |
dc.contributor.alternative | 中川, 英刀 | ja |
dc.contributor.alternative | 藤本, 明洋 | ja |
dc.date.accessioned | 2019-10-29T02:02:52Z | - |
dc.date.available | 2019-10-29T02:02:52Z | - |
dc.date.issued | 2019-10-22 | - |
dc.identifier.issn | 2045-2322 | - |
dc.identifier.uri | http://hdl.handle.net/2433/244393 | - |
dc.description | 血中遊離DNAの高精度解析手法を開発 --リキッドバイオプシーによるゲノム医療へ--. 京都大学プレスリリース. 2019-10-29. | ja |
dc.description.abstract | Plasma cell-free DNA (cfDNA) testing plays an increasingly important role in precision medicine for cancer. However, circulating cell-free tumor DNA (ctDNA) is highly diluted by cfDNA from non-cancer cells, complicating ctDNA detection and analysis. To identify low-frequency variants, we developed a program, eVIDENCE, which is a workflow for filtering candidate variants detected by using the ThruPLEX tag-seq (Takara Bio), a commercially-available molecular barcoding kit. We analyzed 27 cfDNA samples from hepatocellular carcinoma patients. Sequencing libraries were constructed and hybridized to our custom panel targeting about 80 genes. An initial variant calling identified 36, 500 single nucleotide variants (SNVs) and 9, 300 insertions and deletions (indels) across the 27 samples, but the number was much greater than expected when compared with previous cancer genome studies. eVIDENCE was applied to the candidate variants and finally 70 SNVs and 7 indels remained. Of the 77 variants, 49 (63.6%) showed VAF of < 1% (0.20–0.98%). Twenty-five variants were selected in an unbiased manner and all were successfully validated, suggesting that eVIDENCE can identify variants with VAF of ≥ 0.2%. Additionally, this study is the first to detect hepatitis B virus integration sites and genomic rearrangements in the TERT region from cfDNA of HCC patients. We consider that our method can be applied in the examination of cfDNA from other types of malignancies using specific custom gene panels and will contribute to comprehensive ctDNA analysis. | en |
dc.format.mimetype | application/pdf | - |
dc.language.iso | eng | - |
dc.publisher | Springer Nature | en |
dc.rights | © The Author(s) 2019. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. | en |
dc.title | eVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA | en |
dc.type | journal article | - |
dc.type.niitype | Journal Article | - |
dc.identifier.jtitle | Scientific Reports | en |
dc.identifier.volume | 9 | - |
dc.relation.doi | 10.1038/s41598-019-51459-4 | - |
dc.textversion | publisher | - |
dc.identifier.artnum | 15017 | - |
dc.identifier.pmid | 31641155 | - |
dc.relation.url | https://www.kyoto-u.ac.jp/ja/research-news/2019-10-29 | - |
dcterms.accessRights | open access | - |
datacite.awardNumber | 18H04049 | - |
jpcoar.funderName | 日本学術振興会 | ja |
jpcoar.funderName.alternative | Japan Society for the Promotion of Science (JSPS) | en |
出現コレクション: | 学術雑誌掲載論文等 |
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