{"id":"hum0291","version":2,"url":"https://humandbs.dbcls.jp/research/hum0291/v2","datePublished":"2023-09-08","versions":[{"version":1,"datePublished":"2021-12-10"},{"version":2,"datePublished":"2023-09-08"}],"title":{"ja":"網羅的ゲノム解析による膵腫瘍ならびに十二指腸腫瘍、胆道腫瘍の本態解明と新規診断・治療法の開発","en":"Elucidation of molecular mechanisms of tumorigenesis and development of diagnoses and treatments based on comprehensive genomic analyses in pancreatic tumors, duodenal tumors and biliary tumors"},"summary":{"aims":{"ja":"膵腫瘍、十二指腸腫瘍、胆道腫瘍の網羅的ゲノムプロファイリングによる疾患の病態解明","en":"To investigate the molecular mechanisms of tumorigenesis based on the comprehensive genome profiling in pancreatic tumors, duodenal tumors, and biliary tumors"},"methods":{"ja":"全ゲノム解析には凍結サンプルからQIAamp DNA Mini Kitを用いて、また、全エクソーム解析にはFFPEサンプルからQIAamp DNA FFPE Tissue Kitを用いてDNAを抽出した。断片化したDNA（1〜2 µg）に対し、全ゲノム解析ではTruSeq DNA PCR-Free Library Prep Kitを、全エクソーム解析ではTruSeq Exome Library Prep Kit用いてライブラリを調製し、HiSeq 2000/2500にて塩基配列の読み取りを行った。RNAシーケンシングについては、凍結サンプルからIllustra RNAspin Mini RNA Isolation Kitを用いてtotal RNAを抽出した。TruSeq RNA Access Library Prep Kitを用いてライブラリを調製し、HiSeq2500にて塩基配列の読み取りを行った。","en":"Genomic DNA was extracted from frozen tissues using QIAamp DNA Mini Kit for whole-genome sequencing (WGS) or from FFPE tissues using QIAamp DNA FFPE Tissue Kit for whole-exome sequencing (WES). For WGS, short-fragment libraries (insert size 350 bp) were prepared with 1-2 μg aliquots of genomic DNA from tumor and matched non-neoplastic tissues using a TruSeq DNA PCR-Free Library Prep Kit according to the manufacturer's instructions. Paired-end sequencing of the libraries was performed using a HiSeq 2000/2500 sequencer. Whole-exome capture libraries were prepared from tumor and matched non-tumor DNAs using a TruSeq Exome Library Prep Kit, according to the manufacturer's instructions. DNA libraries were sequenced in a paired-end mode with 100-bp reads, using HiSeq 2000/2500 sequencer. Total RNA was extracted from frozen tissues using Illustra RNAspin Mini RNA Isolation Kit. Whole-transcriptome sequencing libraries were prepared using the TruSeq RNA Access Library Prep Kit. Sequencing was performed on HiSeq 2500 sequencer."},"targets":{"ja":"膵腫瘍 57＋6 症例、十二指腸腫瘍 6＋1 症例、胆道腫瘍 11 症例","en":"Pancreatic tumor, Duodenal tumor, Biliary tumors"},"url":{"ja":[{"url":"https://www.med.osaka-u.ac.jp/activities/results/2021year/yachida2021-12-9","text":"https://www.med.osaka-u.ac.jp/activities/results/2021year/yachida2021-12-9"}],"en":[{"url":"https://resou.osaka-u.ac.jp/en/research/2021/20211209_1","text":"https://resou.osaka-u.ac.jp/en/research/2021/20211209_1"}]}},"listingSummary":{"methods":{"ja":"配列決定\n発現","en":"Sequencing, Expression profiling"},"targets":{"ja":"膵腫瘍：57＋6症例\n十二指腸腫瘍：6＋1症例\n胆道腫瘍：11症例\n（日本人）","en":"Pancreatic tumor: 57+6 cases\nDuodenal tumor: 6+1 cases\nBiliary tumors: 11 cases\n(Japanese)"},"typeOfData":{"ja":"NGS\n（WGS、Exome、RNA-seq）","en":"NGS\n(WGS, Exome, RNA-seq)"}},"releaseNote":{"ja":"膵腫瘍、十二指腸腫瘍、胆道腫瘍の腫瘍組織ならびに非腫瘍組織から抽出したRNAを用いたRNAシーケンシング解析データをfastqファイルにて提供する。","en":"RNAs extracted from tumor and non-tumor tissues of patients with pancreatic tumors, duodenal tumors, or biliary tumors were used for the RNA sequencing analysis. Fastq files are provided."},"dataProviders":[{"name":{"ja":"谷内田 真一","en":"Shinichi Yachida"},"organization":{"name":{"ja":"大阪大学大学院 医学系研究科 医学専攻 ゲノム生物学講座・がんゲノム情報学","en":"Cancer Genome Informatics, Department of Genome Biology, Graduate School of Medicine/Faculty of Medicine, Osaka University"}}}],"researchProjects":[{"name":{"ja":"Elucidation of molecular mechanisms of tumorigenesis and development of diagnoses and treatments based on comprehensive genomic analyses in pancreatic tumors, duodenal tumors and biliary tumors","en":"Elucidation of molecular mechanisms of tumorigenesis and development of diagnoses and treatments based on comprehensive genomic analyses in pancreatic tumors, duodenal tumors and biliary tumors"},"url":{"ja":[{"url":"https://www.med.osaka-u.ac.jp/pub/cgi/","text":"https://www.med.osaka-u.ac.jp/pub/cgi/"}],"en":null}}],"grants":[{"title":{"ja":"統合的ゲノム解析による消化器神経内分泌がんの本態解明","en":"Comprehensive genomic characterization of gastroenterological neuroendocrine carcinomas"},"agency":{"ja":"日本医療研究開発機構（AMED） 次世代がん医療創生研究事業（P-CREATE）","en":"Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED)"},"grantIds":["JP17cm0106612"]}],"relatedPublications":[{"title":"Comprehensive Genomic Profiling of Neuroendocrine Carcinomas of the Gastrointestinal System","doi":"https://doi.org/10.1158/2159-8290.CD-21-0669","datasets":["JGAD000473"]}],"datasets":["JGAD000473"],"controlledAccessUsers":[{"principalInvestigator":{"ja":"谷本 梓","en":"Auzsa Tanimoto"},"affiliation":{"ja":"金沢大学 がん進展制御研究所腫瘍内科, 金沢大学","en":"Division of Medical Oncology, Cancer Research Institute, Kanazawa University"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"肺大細胞神経内分泌がん (LCNEC) に対する遺伝子プロファイルに基づいた治療戦略の確立","en":"Strategy for large cell neuroendocrine carcinoma based on gene and molecular subtypes"},"periodStart":"2022-04-07","periodEnd":"2023-10-04","datasets":["JGAD000473"]},{"principalInvestigator":{"ja":"山本 拓也","en":"Takuya Yamamoto"},"affiliation":{"ja":"プレシジョン免疫プロジェクト, 国立研究開発法人 医薬基盤・健康・栄養研究所","en":"Center for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"新規がん抗原の同定に基づく消化器がんおよび悪性黒色腫（メラノーマ）に対するワクチン開発基盤研究\r\n","en":"Basic research for vaccine development against gastrointestinal cancer and malignant melanoma based on the identification of novel cancer antigens\r\n"},"periodStart":"2024-11-12","periodEnd":"2026-03-31","datasets":["JGAD000473"]},{"principalInvestigator":{"ja":"勝田 絵里子","en":"Eriko Katsuta"},"affiliation":{"ja":"肝胆膵外科, 東京科学大学","en":"HBP surgery, Institute of Science Tokyo"},"country":{"ja":"日本","en":"Japan"},"researchTitle":{"ja":"肝胆膵癌の早期発見、進行、予後予測、治療効果予測に関わる因子の研究","en":"Investigation of biomarkers and clinical indicators for early detection, progression, prognosis, and treatment response in hepatobiliary and pancreatic cancers."},"periodStart":"2025-07-03","periodEnd":"2027-05-31","datasets":["JGAD000473"]}]}