{"id":"hum0386","version":1,"url":"https://humandbs.dbcls.jp/research/hum0386/v1","datePublished":"2023-04-11","versions":[{"version":1,"datePublished":"2023-04-11"}],"title":{"ja":"長鎖リードの局所アセンブリによる一塩基解像度でのヒト反復配列のゲノムワイド解析","en":"Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes"},"summary":{"aims":{"ja":"長鎖シークエンスデータはエラー率が高く、取り扱いが確立していない。そのため有用な情報解析手法の確立が重要である。マッピングに基づく解析や全ゲノムアセンブリに基づく変異検出には、反復配列によるエラーや塩基配列情報の欠如など問題がある。また、欠失などに比べ、挿入は多くが反復配列に由来することや配列情報が得にくいことから解析が困難であった。本研究では、ヒトの挿入配列の全容と挿入メカニズムの解明を目的として、長鎖リードに対応した新規解析手法を開発し、さらにそれを適用し、2サンプルの全ゲノム解析を行なった。","en":"Long-read sequencing data has a high error rate, and its handling has not been established. Therefore, it is important to establish useful bioinformatics analysis methods. Mapping-based analysis and whole-genome-assembly-based variant detection have problems such as errors due to repetitive sequences and lack of nucleotide sequence information. Compared to deletions, insertions are difficult to analyze because many of them are derived from repetitive sequences and sequence information is difficult to obtain. In this study, we developed a novel analysis method for long reads and applied it to whole genome analysis of two samples to elucidate the entire human insertion sequence and insertion mechanism."},"methods":{"ja":"NA18943の細胞株から抽出したDNAを、Oxford Nanoporeシークエンサーを用いてシークエンスし、231.6 Gbp（77× coverage）のデータを得た。","en":"We sequenced the genomic DNA of NA18943 from a B cell line using a single platform, MinION. The sequencing data totaled 231.6 Gbp (77× coverage)."},"targets":{"ja":"NA18943はHapMap計画で用いられた健常者の細胞株由来のDNAサンプルである。本研究において、申請者らはOxford Nanoporeシークエンサーを用いてNA18943の全ゲノムシークエンスを行った。","en":"NA18943 is a healthy sample used in the HapMap project. We performed whole genome sequencing of NA18943 using Oxford Nanopore sequencer."},"url":{"ja":null,"en":null}},"listingSummary":{"methods":{"ja":"配列決定","en":"Sequencing"},"targets":{"ja":"HapMap：1検体\n（細胞株）","en":"HapMap: 1 sample\n(Cell-line)"},"typeOfData":{"ja":"NGS\n（WGS）","en":"NGS\n(WGS)"}},"releaseNote":{"ja":"HapMap日本人検体（NA18943）を対象とし、長鎖シークエンサー（nanopore）による全ゲノムシークエンスを行った。fastqファイルを提供する。","en":"A HapMap DNA sample (NA18943) was used for whole genome sequencing with Nanopore sequencer. A fastq file is provided."},"dataProviders":[{"name":{"ja":"藤本 明洋","en":"Akihiro Fujimoto"},"organization":{"name":{"ja":"東京大学 医学系研究科","en":"Graduate School of Medicine,The University of Tokyo"}}}],"researchProjects":[{"name":{"ja":"人類遺伝学分野","en":"Department of Human Genetics"},"url":{"ja":[{"url":"https://www.humgenet.m.u-tokyo.ac.jp","text":"https://www.humgenet.m.u-tokyo.ac.jp"}],"en":[{"url":"https://www.humgenet.m.u-tokyo.ac.jp/index.en.html","text":"https://www.humgenet.m.u-tokyo.ac.jp/index.en.html"}]}}],"grants":[{"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":"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"]},{"title":{"ja":"ヤポネシア人の人口推定を中心とした巨大データ解析","en":"Deciphering Origin and Establishment of Japonesians mainly based on genome sequence data"},"agency":{"ja":"科学研究費助成事業 新学術領域研究（研究領域提案型）","en":"KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)"},"grantIds":["18H05511"]}],"relatedPublications":[{"title":"Localized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes","doi":"https://doi.org/10.1186/s40246-023-00467-7","datasets":["DRA015813"]}],"datasets":["DRA015813"],"controlledAccessUsers":[]}