NBDC Research ID: hum0291.v2
SUMMARY
Aims: To investigate the molecular mechanisms of tumorigenesis based on the comprehensive genome profiling in pancreatic tumors, duodenal tumors, and biliary tumors
Methods: 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.
Participants/Materials: Pancreatic tumor, Duodenal tumor, Biliary tumors
URL: https://resou.osaka-u.ac.jp/en/research/2021/20211209_1
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000359 | NGS (WGS, Exome) | Controlled-access (Type I) | 2021/12/10 |
| JGAS000359 (data addition) | NGS (RNA-seq) | Controlled-access (Type I) | 2023/09/08 |
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MOLECULAR DATA
| Participants/Materials |
Pancreatic tumor (ICD10: C25): 33 cases Duodenal tumor (ICD10: C170): 2 cases Biliary tumors (ICD10: C240): 1 case |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | DNAs extracted from frozen samples (tumor and matched non-tumor tissues) |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq DNA PCR-Free Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S2 or E220ev) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000473 |
| Total Data Volume | 12.8 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pancreatic tumor (ICD10: C25): 24 cases Duodenal tumor (ICD10: C170): 4 cases Biliary tumors (ICD10: C240): 10 cases |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | DNAs extracted from FFPE samples (tumor and matched non-tumor tissues) |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Exome Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S2 or E220ev) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000473 |
| Total Data Volume | 12.8 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pancreatic tumor (ICD10: C25): 43 cases tumor tissue: 43 samples, non-tumor tissue: 3 samples Duodenal tumor (ICD10: C170): 4 cases tumor tissue: 5 samples, non-tumor tissue: 1 sample Biliary tumors (ICD10: C240): 1 case tumor tissue: 1 sample |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor or non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq RNA Access Library Prep Kit |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000473 |
| Total Data Volume | 361.7 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shinichi Yachida
Affiliation: Cancer Genome Informatics, Department of Genome Biology, Graduate School of Medicine/Faculty of Medicine, Osaka University
Project / Group Name: 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
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Comprehensive genomic characterization of gastroenterological neuroendocrine carcinomas | JP17cm0106612 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Comprehensive Genomic Profiling of Neuroendocrine Carcinomas of the Gastrointestinal System | doi: 10.1158/2159-8290.CD-21-0669 | JGAD000473 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Auzsa Tanimoto | Division of Medical Oncology, Cancer Research Institute, Kanazawa University | Strategy for large cell neuroendocrine carcinoma based on gene and molecular subtypes | JGAD000473 | 2022/04/01-2023/03/31 |
