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 ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000557 | Controlled-access (Type I) | 2022/11/30 | |
| JGAS000557 (data deleted) | Controlled-access (Type I) | 2023/01/11 | |
| JGAS000557 (data added) | Controlled-access (Type I) | 2023/02/15 | |
| JGAS000609 | Controlled-access (Type I) | 2023/08/09 | |
| JGAS000610 | Controlled-access (Type I) | 2023/08/09 | |
| JGAS000609 (data added) | Controlled-access (Type I) | 2024/06/05 | |
| JGAS000610 (data added) | Controlled-access (Type I) | 2024/06/05 |
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MOLECULAR DATA
| 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 |
| 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 | |
| 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 |
| 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 | |
| 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 |
| 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 | |
| Total Data Volume |
JGAD000678: 3 TB (fastq) JGAD000738: 384.8 + 207.3 GB (fastq) JGAD000739: 471.8 GB (fastq) |
| Comments (Policies) | NBDC policy |
| 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):
| Name | Title | Project 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
| Title | DOI | Dataset 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 Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
