{"id":"hum0364","version":1,"url":"https://humandbs.dbcls.jp/research/hum0364/v1","datePublished":"2022-08-29","versions":[{"version":1,"datePublished":"2022-08-29"}],"title":{"ja":"ヒトのマイクロサテライト多型の包括的解析","en":"Comprehensive analysis of microsatellite polymorphisms in human populations"},"summary":{"aims":{"ja":"次世代シークエンス技術（NGS）により全ゲノムシーケンス（WGS）解析が可能になり、一塩基変異、挿入・欠失、コピー数変異、構造変異などの遺伝子変異を同定できるようになった。 しかし、リード長が短く、リピート領域でのシーケンスエラー率が高いため、マイクロサテライト（MS）領域の変異や多型の同定は困難であった。本研究では、ヒトのMS多型の全容を明らかにするため、公開されている2つの大規模なヒトゲノムシーケンスデータセット（Simons Genome Diversity Project [SGDP]、Human Genome Diversity Project [HGDP]）および縄文人の全ゲノムデータについて、以前開発したMS検出法（MIVcall法）を用いて約900万個のMS領域の解析を行った。","en":"Next generation sequencing technologies (NGS) enable whole genome sequencing (WGS) analysis. In the past decade, applications of NGS and the development of algorithms for the analysis have successfully identified various types of genetic variations. However, due to the short read length and the high sequencing error rate in repeat regions, the identification of mutations and polymorphisms in microsatellite (MS) regions has been difficult. In this study, we analyzed approximately nine million MS regions using a previously developed MS caller (MIVcall) for three large publicly available human genome sequencing data sets: Simons Genome Diversity Project (SGDP), and Human Genome Diversity Project (HGDP)."},"methods":{"ja":"MIVcall法を用いたMS多型の検出","en":"MS regions were detected by MIVcall method"},"targets":{"ja":"非制限公開されているWGS解析データをダウンロードし、データの質の評価をクリアしたSGDP 276サンプル、 HGDP 693サンプル、縄文人 1サンプル（全て健常者由来）","en":"Publicly available whole genome sequencing data of healthy individuals were downloaded and used for MS analysis. After evaluating the quality of the data, we analyzed 276 samples from SGDP, 693 from HGDP, and one Jomon Individual (F23)."},"url":{"ja":null,"en":null}},"listingSummary":{"methods":{"ja":"配列決定","en":"Sequencing"},"targets":{"ja":"Simons Genome Diversity Project（SGDP）：276名\nHuman Genome Diversity Project（HGDP）：693名\n縄文人：1名","en":"Simons Genome Diversity Project (SGDP): 276 samples\nHuman Genome Diversity Project (HGDP): 693 samples\nJomon Individual: 1 individual"},"typeOfData":{"ja":"NGS\n（WGS）","en":"NGS\n(WGS)"}},"releaseNote":{"ja":"非制限公開されているSimons Genome Diversity Project（SGDP）276サンプル、Human Genome Diversity Project（HGDP）693サンプル、縄文人1サンプル（F23）のWGS解析データについて、MIVcall法を用いて検出した733900個のマイクロサテライト（MS）多型情報をvcfファイルにて提供する。","en":"Whole genome sequencing data (Simons Genome Diversity Project [SGDP], Human Genome Diversity Project [HGDP], Jomon Individual) were downloaded and used for MS analysis by using of MIVcall method. Individual MS data are provided as a vcf file."},"dataProviders":[{"name":{"ja":"藤本 明洋","en":"Akihiro Fujimoto"},"organization":{"name":{"ja":"東京大学大学院 医学系研究科 人類遺伝学教室","en":"School of Integrated Health Sciences, Faculty of Medicine, The University of Tokyo"}}}],"researchProjects":[],"grants":[{"title":{"ja":"ゲノム配列を核としたヤポネシア人の起源と成立の解明","en":"Deciphering Origin and Establishment of Japonesians mainly based on genome sequence data"},"agency":{"ja":"科学研究費補助金 新学術領域研究","en":"KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)"},"grantIds":["18H05511"]},{"title":{"ja":"マイクロサテライトを用いた人類集団史の推定","en":"Comprehensive analysis of microsatellite polymorphism in the human population"},"agency":{"ja":"科学研究費補助金 挑戦的研究 （萌芽）","en":"Grant-in-Aid for Scientific Research on Innovative Areas from Japan Society for the Promotion of Science (JSPS)"},"grantIds":["18H02680"]},{"title":{"ja":"先進的シークエンス情報解析技術基盤の開発","en":"Development of advanced data analysis methods for genome sequencing"},"agency":{"ja":"国立研究開発法人日本医療研究開発機構（AMED） ゲノム医療実現推進プラットフォーム事業","en":"Platform Program for Promotion of Genome Medicine, Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP20km0405207"]}],"relatedPublications":[],"datasets":["NHA000176"],"controlledAccessUsers":[]}