NBDC Research ID: hum0419.v3

 

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

 

Dataset IDType of DataCriteriaRelease 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

*Release Note 

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MOLECULAR DATA

Exome (JGAS000641)

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)

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 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

Total Data Volume

JGAD000783: 8.5 GB (bam, bai)

JGAD000794: 9.4 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

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):

NameTitleProject 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

TitleDOIDataset 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

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use