NBDC Research ID: hum0419.v4
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, a patient with mucus-producing solid-dominant adenocarcinoma of lung and a patient with pulmonary adenocarcinoma harboring EML4-ALK variant 3, organoids established from patients with esophageal cancer
| 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 |
| JGAS000664 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2024/06/17 |
| JGAS000749 | NGS (Exome) | Controlled-access (Type I) | 2025/03/21 |
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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 |
Exome (JGAS000653, JGAS000664, JGAS000749)
| Participants/Materials |
mucus-producing solid-dominant adenocarcinoma of lung (ICD10: C34.1, C34.3): 1 case tumor-derived organoids: 1 sample pulmonary adenocarcinoma harboring EML4-ALK variant 3 (ICD10: C34.1, C34.3): 1 case tumor-derived organoids: 1 sample esophageal cancer (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 |
| 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 |
mucus-producing solid-dominant adenocarcinoma of lung: JGAD000783 pulmonary adenocarcinoma harboring EML4-ALK variant 3: JGAD000794 esophageal cancer: JGAD000884 |
| Total Data Volume |
JGAD000783: 8.5 GB (bam, bai) JGAD000794: 9.4 GB (bam, bai) JGAD000884: 21.6 GB (bam, bai) |
| Comments (Policies) | NBDC policy |
RNA-seq (JGAS000653, JGAS000664)
| Participants/Materials |
mucus-producing solid-dominant adenocarcinoma of lung (ICD10: C34.1, C34.3): 1 case tumor-derived organoids: 1 sample pulmonary adenocarcinoma harboring EML4-ALK variant 3 (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 |
mucus-producing solid-dominant adenocarcinoma of lung: JGAD000783 pulmonary adenocarcinoma harboring EML4-ALK variant 3: JGAD000794 |
| Total Data Volume |
JGAD000783: 8.5 GB (bam, bai) JGAD000794: 9.4 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 |
| 3 | Transforming tumoroids derived from ALK-positive pulmonary adenocarcinoma to squamous cell carcinoma in vivo | doi: 10.1007/s13577-024-01085-8 | JGAD000794 |
| 4 | Establishment and characterization of novel patient-derived esophageal tumoroids with long-term cultivability | doi: 10.1007/s13577-025-01206-x | JGAD000884 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
