NBDC Research ID: hum0357.v5

 

SUMMARY

Aims: To develop new treatments for pulmonary diseases by using NGS analyses data 

Methods: Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), ATAC-seq, and methylation array analyses with DNA harvested from lung cancer organoids established from surgery, biopsy, pleural effusion, sputum, and peripheral blood samples of patients. RNA-seq analysis with RNA harvested from lung cancer organoids established from surgery, biopsy, pleural effusion, sputum, normal lung organoids and peripheral blood samples of patients.

Participants/Materials: Lung cancer

 

Dataset IDType of DataCriteriaRelease Date
JGAS000557

NGS (WGS)

NGS (Exome)

NGS (RNA-seq)

NGS (ATAC-seq)

Methylation array

Controlled-access (Type I) 2022/11/30
JGAS000557 (data deleted)

NGS (WGS)

NGS (RNA-seq)

NGS (ATAC-seq)

Methylation array

Controlled-access (Type I) 2023/01/11
JGAS000557 (data added)

NGS (WGS)

NGS (RNA-seq)

NGS (ATAC-seq)

Methylation array

Controlled-access (Type I) 2023/02/15
JGAS000609

NGS (Exome)

NGS (RNA-seq)

NGS (ATAC-seq)

Controlled-access (Type I) 2023/08/09
JGAS000610

NGS (Exome)

NGS (RNA-seq)

NGS (ATAC-seq)

Controlled-access (Type I) 2023/08/09
JGAS000609 (data added)

NGS (Exome)

NGS (RNA-seq)

NGS (ATAC-seq)

Controlled-access (Type I) 2024/06/05
JGAS000610 (data added)

NGS (Exome)

NGS (RNA-seq)

Controlled-access (Type I) 2024/06/05

*Release Note

* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

WGS

Participants/Materials lung cancer (ICD10: C349): 22 cases
Targets WGS
Target Loci for Capture Methods -
Platform Illumina [NovaSeq 6000]
Library Source DNAs extracted from organoids established from tumor tissues
Cell Lines -
Library Construction (kit name) SureSelect Human All Exon V6 kit
Fragmentation Methods Ultrasonic fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD00678
Total Data Volume 3 TB (fastq)
Comments (Policies) NBDC policy

 

Exome

Participants/Materials

lung cancer (ICD10: C349)

[organoids]

JGAS000557 / JGAD000678: 21 cases

JGAS000609 / JGAD000738: 27 + 6 cases (30 + 10 samples)

(8 normal lung organoids from 6 cases are included in 27 cases)

JGAS000610 / JGAD000739: 25 + 4 cases (31 + 5 samples)

[tumor tissues]

JGAS000609 / JGAD000738: 10 cases (10 samples)

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000]
Library Source DNAs extracted from tumor tissues or organoids established from tumor or normal tissues
Cell Lines -
Library Construction (kit name) SureSelect Human All Exon V6 kit
Fragmentation Methods Ultrasonic fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Japanese Genotype-phenotype Archive Dataset ID

JGAD000678

JGAD000738

JGAD000739

Total Data Volume

JGAD000678: 3 TB (fastq)

JGAD000738: 384.8 + 207.3 GB (fastq)

JGAD000739: 471.8 + 38.4 GB (fastq)

Comments (Policies) NBDC policy

 

RNA-seq

Participants/Materials

lung cancer (ICD10: C349)

[organoids]

JGAS000557 / JGAD000678: 43 cases

JGAS000609 / JGAD000738: 33 + 6 cases (38 + 10 samples)

JGAS000610 / JGAD000739: 25 + 4 cases (31 + 5 samples)

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [NovaSeq 6000]
Library Source RNAs extracted from organoids established from tumor tissues
Cell Lines -
Library Construction (kit name) TruSeq RNA Library Prep Kit v2
Fragmentation Methods TruSeq RNA Library Prep Kit v2
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Japanese Genotype-phenotype Archive Dataset ID

JGAD000678

JGAD000738

JGAD000739

Total Data Volume

JGAD000678: 3 TB (fastq)

JGAD000738: 384.8 + 207.3 GB (fastq)

JGAD000739: 471.8 + 38.4 GB (fastq)

Comments (Policies) NBDC policy

 

ATAC-seq

Participants/Materials

lung cancer (ICD10: C349)

[organoids]

JGAS000557 / JGAD000678: 42 cases

JGAS000609 / JGAD000738: 14 + 2 cases (14 + 3 samples)

JGAS000610 / JGAD000739: 25 cases (28 samples)

Targets ATAC-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq X Ten]
Library Source DNAs extracted from organoids established from tumor tissues
Cell Lines -
Library Construction (kit name) Nextera XT DNA Library Preparation Kit
Fragmentation Methods Tn5 transposase
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Japanese Genotype-phenotype Archive Dataset ID

JGAD000678

JGAD000738

JGAD000739

Total Data Volume

JGAD000678: 3 TB (fastq)

JGAD000738: 384.8 + 207.3 GB (fastq)

JGAD000739: 471.8 GB (fastq)

Comments (Policies) NBDC policy

 

Methylation array

Participants/Materials lung cancer (ICD10: C349): 42 cases
Targets Methylation array
Target Loci for Capture Methods -
Platform Illumina [Infinium MethylationEPIC BeadChip]
Source DNAs extracted from organoids established from tumor tissues
Cell Lines -
Reagents (Kit, Version) Infinium MethylationEPIC microarray
Probe Number 850,000
Japanese Genotype-phenotype Archive Dataset ID JGAD00678
Total Data Volume 3 TB (idat)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Hiroyuki Yasuda

Affiliation: Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) Clarification of heterogeneity of lung cancer and identification of novel therapeutic targets using lung cancer organoid library JP21cm0106576
Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) Clarification of molecular mechanisms creating phenotypic diversity of lung cancer using patient-derived organoid library JP22ck0106722
KAKENHI Grant-in-Aid for Scientific Research (B) Clarification of signal alteration mechanisims of lung cancer using lung cancer organoid library 21H02765
KAKENHI Grant-in-Aid for Scientific Research (C) Establishment of lung cancer and normal lung organoid library 19K08610
KAKENHI Grant-in-Aid for Scientific Research (C) Clarification of carcinogenesis process of small cell lung cancer using patient-derived organoid library 22K08290

 

PUBLICATIONS

TitleDOIDataset ID
1 Genotype-phenotype mapping of a patient-derived lung cancer organoid biobank identifies NKX2-1-defined Wnt dependency in lung adenocarcinoma doi: 10.1016/j.celrep.2023.112212 JGAD000678
2

 

USRES (Controlled-access Data)

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