NBDC Research ID: hum0291.v1

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 a QIAamp DNA Mini Kit for whole-genome sequencing (WGS) or from FFPE tissues using a 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 a HiSeq 2000/2500 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

*Release Note

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MOLECULAR DATA

WGS


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

Exome


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

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