NBDC Research ID: hum0419.v1
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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 analysis
Participants/Materials: Three kinds of organoids were established from a patient with pulmonary large-cell neuroendocrine carcinoma
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000641 | NGS (Exome) | Controlled-access (Type I) | 2024/04/24 |
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MOLECULAR DATA
| Participants/Materials |
pulmonary large cell neuroendocrine carcinoma (ICD10: C34.1, C34.3): 3 case 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 |
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 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
