NBDC Research ID: hum0419.v2
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SUMMARY
Aims: We generated organoids derived from gastrointestinal cancer and intra-thoracic malignancy, and selected effective anticancer agents and molecular targeted drugs based on genome analysis. In addition, we analyze their antitumor effects and construct a drug evaluation system for personalized medicine. Furthermore, by genetically modifying normal lung organoids, we elucidate the molecular mechanisms involved in the carcinogenesis of lung cancer.
Methods: Whole exome sequencing and RNA sequencing analysis
Participants/Materials:Organoids established from patients with pulmonary large-cell neuroendocrine carcinoma and a patient with mucus-producing solid-dominant adenocarcinoma of lung
Dataset ID | Type of Data | Criteria | Release Date |
---|---|---|---|
JGAS000641 | NGS (Exome) | Controlled-access (Type I) | 2024/04/24 |
JGAS000653 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2024/05/08 |
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MOLECULAR DATA
Participants/Materials |
pulmonary large cell neuroendocrine carcinoma (ICD10: C34.1, C34.3): 3 cases tumor-derived organoids: 3 samples |
Targets | Exome |
Target Loci for Capture Methods | - |
Platform | Illumina [NovaSeq 6000] |
Library Source | DNAs extracted from tumor-derived organoids |
Cell Lines | - |
Library Construction (kit name) | SureSelect XT Human All Exon V6 Kit, SureSelect XT Reagents |
Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
Spot Type | Paired-end |
Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 151 bp |
Mapping Methods | DRAGEN Bio-IT Platform 3.9.5 |
Mapping Quality | Reads with MAPQ >= 40: 93.51% |
Reference Genome Sequence | hg19 |
Coverage (Depth) | 98.21 depth |
Japanese Genotype-phenotype Archive Dataset ID | JGAD000771 |
Total Data Volume | 22.9 GB (bam, bai, vcf, tbi) |
Comments (Policies) | NBDC policy |
Participants/Materials |
mucus-producing solid-dominant adenocarcinoma of lung (ICD10: C34.1, C34.3): 1 case tumor-derived organoids: 1 sample |
Targets | Exome |
Target Loci for Capture Methods | - |
Platform | Illumina [NovaSeq 6000] |
Library Source | DNAs extracted from tumor-derived organoids |
Cell Lines | - |
Library Construction (kit name) | SureSelect XT Human All Exon V6 Kit |
Fragmentation Methods | Ultrasonic fragmentation |
Spot Type | Paired-end |
Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 151 bp |
Mapping Methods | DRAGEN Bio-IT Platform 3.9.5 |
Mapping Quality | - |
Reference Genome Sequence | hg19 |
Coverage (Depth) | 98.21 depth |
Japanese Genotype-phenotype Archive Dataset ID | JGAD000783 |
Total Data Volume | 8.5 GB (bam, bai) |
Comments (Policies) | NBDC policy |
Participants/Materials |
mucus-producing solid-dominant adenocarcinoma of lung (ICD10: C34.1, C34.3): 1 case tumor-derived organoids: 1 sample |
Targets | RNA-seq |
Target Loci for Capture Methods | - |
Platform | Illumina [NovaSeq 6000] |
Library Source | RNAs extracted from tumor-derived organoids |
Cell Lines | - |
Library Construction (kit name) | TruSeq Stranded mRNA Library Prep Kit |
Fragmentation Methods | Exposure to divalent cations at elevated temperatures |
Spot Type | Paired-end |
Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 101 bp |
Mapping Methods | STAR-Fusion v1.9.0 |
Mapping Quality | - |
Reference Genome Sequence | hg19 |
Japanese Genotype-phenotype Archive Dataset ID | JGAD000783 |
Total Data Volume | 8.5 GB (bam, bai) |
Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takuya Fukazawa
Affiliation: Department of General Surgery, Kawasaki Medical School
Project / Group Name: -
Funds / Grants (Research Project Number):
Name | Title | Project Number |
---|---|---|
KAKENHI Grant-in-Aid for Scientific Research (C) | Elucidation of mechanism of carcinogenesis s and progression in lung squamous cell carcinoma with organoid technology | 22H03164 |
KAKENHI Grant-in-Aid for Scientific Research (B) | Elucidation of the molecular pathogenesis and carcinogenic mechanisms of pulmonary neuroendocrine tumors using organoids | 19K07699 |
PUBLICATIONS
Title | DOI | Dataset ID | |
---|---|---|---|
1 | Patient-derived tumoroid models of pulmonary large-cell neuroendocrine carcinoma: A promising tool for personalized medicine and developing novel therapeutic strategies | doi: 10.1016/j.canlet.2024.216816 | JGAD000771 |
2 | Establishment and characterization of novel high mucus-producing lung tumoroids derived from a patient with pulmonary solid adenocarcinoma | doi: 10.1007/s13577-024-01060-3 | JGAD000783 |
USRES (Controlled-access Data)
Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
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