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Comparison of Causative Variant Prioritization Tools Using Next-generation Sequencing Data in Japanese Patients with Mendelian Disorders
https://repository.lib.tottori-u.ac.jp/records/4796
https://repository.lib.tottori-u.ac.jp/records/4796ec1e9efa-c5af-44a5-945c-04f80364fdb8
| 名前 / ファイル | ライセンス | アクション |
|---|---|---|
yam62(3)_244.pdf (1.7 MB)
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| Item type | 学術雑誌論文 / Journal Article(1) | |||||
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| 公開日 | 2019-12-05 | |||||
| タイトル | ||||||
| タイトル | Comparison of Causative Variant Prioritization Tools Using Next-generation Sequencing Data in Japanese Patients with Mendelian Disorders | |||||
| 言語 | en | |||||
| 言語 | ||||||
| 言語 | eng | |||||
| キーワード | ||||||
| 主題 | computational biology | |||||
| キーワード | ||||||
| 主題 | databases | |||||
| キーワード | ||||||
| 主題 | genetic | |||||
| キーワード | ||||||
| 主題 | whole exome sequencing | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題 | computational biology | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題 | databases | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題 | genetic | |||||
| キーワード | ||||||
| 言語 | en | |||||
| 主題 | whole exome sequencing | |||||
| 資源タイプ | ||||||
| 資源タイプ | journal article | |||||
| 著者 |
Ebiki, Matsutaka
× Ebiki, Matsutaka× Okazaki, Tetsuya× Kai, Masachika× Adachi, Kaori× Namba, Eiji |
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| 著者所属（英） | ||||||
| 言語 | en | |||||
| 値 | The Development of Innovative Future Medical Treatment, Graduate School of Medical Sciences, Tottori University | |||||
| 著者所属（英） | ||||||
| 言語 | en | |||||
| 値 | Division of Child Neurology, Department of Brain and Neurosciences, School of Medicine, Tottori University Faculty of Medicine / Division of Clinical Genetics, Tottori University Hospital / Technical Department, Tottori University | |||||
| 著者所属（英） | ||||||
| 言語 | en | |||||
| 値 | Research Initiative Center, Organization for Research Initiative and Promotion, Tottori University | |||||
| 著者所属（英） | ||||||
| 言語 | en | |||||
| 値 | Research Strategy Division, Organization for Research Initiative and Promotion, Tottori University | |||||
| 著者所属（英） | ||||||
| 言語 | en | |||||
| 値 | Division of Clinical Genetics, Tottori University Hospital / Technical Department, Tottori University / Research Strategy Division, Organization for Research Initiative and Promotion, Tottori University | |||||
| 抄録 | ||||||
| 内容記述タイプ | Other | |||||
| 内容記述 | Background: During the investigation of causative variants of Mendelian disorders using next-generation sequencing, the enormous number of possible candidates makes the detection process complex, and the use of multidimensional methods is required. Although the utility of several variant prioritization tools has been reported, their effectiveness in Japanese patients remains largely unknown. Methods: We selected 5 free variant prioritization tools (PhenIX, hiPHIVE, Phen-Gen, eXtasy-order statistics, and eXtasy-combined max) and assessed their effectiveness in Japanese patient populations. To compare these tools, we conducted 2 studies: one based on simulated data of 100 diseases and another based on the exome data of 20 in-house patients with Mendelian disorders. To this end we selected 100 pathogenic variants from the “Database of Pathogenic Variants (DPV)” and created 100 variant call format (VCF) files that each had pathogenic variants based on reference human genome data from the 1000 Genomes Project. The later “in-house” study used exome data from 20 Japanese patients with Mendelian disorders. In both studies, we utilized 1-5 terms of “Human Phenotype Ontology” as clinical information. Results: In our analysis based on simulated disease data, the detection rate of the top 10 causative variants was 91% for hiPHIVE, and 88% for PhenIX, based on 100 sets of simulated disease VCF data. Also, both software packages detected 82% of the top 1 causative variants. When we used data from our in-house patients instead, we found that these two programs (PhenIX and hiPHIVE) produced higher detection rates than the other three systems in our study. The detection rate of the top 1 causative variant was 71.4% for PhenIX, 65.0% for hiPHIVE. Conclusion: The rates of detecting causative variants in two Exomizer software packages, hiPHIVE and PhenIX, were higher than for the other three software systems we analyzed, with respect to Japanese patients. | |||||
| 書誌情報 |
Yonago Acta Medica en : Yonago Acta Medica 巻 62, 号 3, p. 244-252, 発行日 2019-09-13 |
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| 雑誌内区分 | ||||||
| 値 | Original Article | |||||
| 出版者 | ||||||
| 出版者 | Tottori University Medical Press | |||||
| ISSN | ||||||
| 収録物識別子タイプ | ISSN | |||||
| 収録物識別子 | 05135710 | |||||
| 書誌レコードID | ||||||
| 収録物識別子タイプ | NCID | |||||
| 収録物識別子 | AA00892882 | |||||
| DOI | ||||||
| 関連タイプ | isIdenticalTo | |||||
| 識別子タイプ | DOI | |||||
| 関連識別子 | 10.33160/yam.2019.09.001 | |||||
| 権利 | ||||||
| 権利情報 | Yonago Acta medica 編集委員会 | |||||
| 情報源 | ||||||
| 関連名称 | Ebiki M, Okazaki T, Kai M, Adachi K, Nanba E. Comparison of Causative Variant Prioritization Tools Using Next-generation Sequencing Data in Japanese Patients with Mendelian Disorders. Yonago Acta Medica. 2019;62:244-252. | |||||
| 関連サイト | ||||||
| 識別子タイプ | URI | |||||
| 関連識別子 | http://www.lib.tottori-u.ac.jp/yam/yam/yam62-3/62-3contents.html | |||||
| 関連名称 | http://www.lib.tottori-u.ac.jp/yam/yam/yam62-3/62-3contents.html | |||||
| 関連サイト | ||||||
| 識別子タイプ | URI | |||||
| 関連識別子 | https://www.jstage.jst.go.jp/article/yam/62/3/62_2019.09.001/_article/ | |||||
| 関連名称 | https://www.jstage.jst.go.jp/article/yam/62/3/62_2019.09.001/_article/ | |||||
| 著者版フラグ | ||||||
| 出版タイプ | VoR | |||||
| EISSN | ||||||
| 値 | 1346-8049 | |||||
