NBDC Research ID: hum0094.v2
Click to Latest version.
SUMMARY
Aims: Identification of oncogenic alteration in breast cancer and lung adenocarcinoma through genomic analysis.
Methods: Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), and RNA-seq were performed with HiSeq 2000/2500.
Participants/Materials: Surgically resected breast cancer tissues and paired non-tumor tissues or peripheral blood cells (as normal tissues)
WES: Triple negative breast cancer: 36 cases (including 16 cases used for WGS and 23 cases used for RNA-seq)
Lung adenocarcinoma : 43 cases
WGS: Triple negative breast cancer: 16 cases
RNA-seq: Triple negative breast cancer: 23 cases
Estrogen receptor-positive breast cancer: 17 cases
Human epidermal growth factor receptor 2 (HER2)-positive breast cancer: 15 cases
Lung adenocarcinoma : 43 cases
URL： https://www.ncc.go.jp/en/ri/division/genetics/index.html
| Data Set ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000095 | NGS (WGS, Exome, RNA-seq) | Controlled Access (Type I) | 2017/09/04 |
| JGAS000105 | NGS (Exome, RNA-seq) | Controlled Access (Type I) | 2018/01/22 |
* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more
MOLECULAR DATA
| Participants/Materials | Triple negative breast cancer (ICD10: C50): 16 cases |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | DNAs extracted from tumor tissues and paired non-tumor tissues or peripheral blood cells as non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext® Ultra™ DNA Library Prep Kit for Illumina® |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 103 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000095 |
| Total Data Volume | 8 TB (bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Triple negative breast cancer (ICD10: C50): 36 cases Lung adenocarcinoma (ICD10: C349): 43 cases |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | DNAs extracted from tumor tissues and paired non-tumor tissues or peripheral blood cells as non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext® Ultra™ DNA Library Prep Kit for Illumina®, SureSelect Human All Exon V5 |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 103 bp |
| Japanese Genotype-phenotype Archive Data set ID |
Triple negative breast cancer: JGAD000095 Lung adenocarcinoma: JGAD000110 (bam) |
| Total Data Volume | 10 TB (bam [ref: hg19/hg38]) |
| Comments (Policies) |
NBDC policy (JGAD000095) NBDC policy & Company User Limit (JGAD000110) |
| Participants/Materials |
Triple negative breast cancer (ICD10: C50): 23 cases Estrogen receptor-positive breast cancer (ICD10: C50): 17 cases HER2-positive breast cance (ICD10: C50)r: 15 cases Lung adenocarcinoma (ICD10: C349): 43 cases |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 103 bp |
| Japanese Genotype-phenotype Archive Data set ID |
Breast cancers: JGAD000095 Lung adenocarcinoma: JGAD000111 (fastq) |
| Total Data Volume | 10 TB (fastq) |
| Comments (Policies) |
NBDC policy (JGAD000095) NBDC policy & Company User Limit (JGAD000111) |
DATA PROVIDER
Principal Investigator: Hiroyuki Mano
Affiliation: Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo
Project / Group Name: -
URL： https://www.ncc.go.jp/en/ri/division/genetics/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Leading Advanced Projects for medical innovation, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-LEAP) | Project for novel therapeutic targets in cancer | - |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Oncogenic mutations of RAC small GTPases in Human cancers | 26430106 |
| Grant from The Princess Takamatsu Cancer Research Fund | Analysis of molecular mechanisms of oncogenic activity of RAC small GTPase | - |
PUBLICATIONS
| Title | DOI | Data Set ID | |
|---|---|---|---|
| 1 | Integrative analysis of genomic alterations in triple-negative breast cancer in association with homologous recombination deficiency | doi: 10.1371/journal.pgen.1006853 | JGAD000095 |
| 2 | Inactivating mutations and hypermethylation of the NKX2-1/TTF-1 gene in non-terminal respiratory unit-type lung adenocarcinomas. | doi: 10.1111/cas.13313 | JGAD000110, JGAD000111 |
USERS (Controlled-Access Data)
| Principal Investigator: | Affiliation: | Data in Use (Data Set ID) | Period of Data Use |
|---|---|---|---|
| Subhajyoti De | Rutgers Cancer Institute, Rutgers the State University of New Jersey | JGAD000095 | 2018/08/06-2021/05/31 |
| Youping Deng | Department of Complementary and Integrative Medicine, University of Hawai Manoa | JGAD000110, JGAD000111 | 2018/10/04-2025/07/10 |
