NBDC Research ID: hum0094.v4
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SUMMARY
Aims: Identification of oncogenic alteration in breast cancer, lung adenocarcinoma and colorectal cancer (CRC) through genomic analysis.
Methods: Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), RNA-seq were performed with HiSeq 2000/2500. Methylation analysis was performed with Infinium MethylationEPIC Kit. SNP array was performed with HumanOmni2.5-8.
Participants/Materials: Surgically resected breast cancer, lung adenocarcinoma and CRC 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
MSI-H CRC: 149 cases
CRC with liver metastasis: 12 cases, CRC without liver metastasis: 16 casess
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
MSI-H CRC: 94 cases
CRC with liver metastasis: 12 cases, CRC without liver metastasis: 16 cases
RNA access: MSI-H CRC: 18 cases
Methylation array: MSI-H CRC: 93 cases
SNP array: MSI-H CRC: 25 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 |
| JGAS000113 |
NGS (Exome, RNA-seq, RNA access), |
Controlled Access (Type I) | 2019/02/12 |
| JGAS000128 | NGS (Exome, RNA-seq) | Controlled Access (Type I) | 2020/08/14 |
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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 | 8.94 TB (bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Triple negative breast cancer (ICD10: C50): 36 cases Lung adenocarcinoma (ICD10: C349): 43 cases MSI-H CRC (ICD10: C18, 19, 20): 149 cases CRC with liver metastasis: 12 cases, CRC without liver metastasis: 16 cases (ICD10: C18, 19, 20) |
| 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) |
breast cancer and lung adenocarcinoma: 103 bp MSI-H CRC: 104 bp or 135 bp CRC: 100 bp or 103 bp |
| Japanese Genotype-phenotype Archive Data set ID |
Triple negative breast cancer: JGAD000095 Lung adenocarcinoma: JGAD000110 (bam) MSI-H CRC: JGAD000122 (bam) CRC: JGAD000139 (bam) |
| Total Data Volume |
JGAD000095: 8.94 TB (bam [ref: hg19]) JGAD000110: 955.16 GB (bam [ref: hg19/hg38]) JGAD000122: 5.99 TB (bam [ref: hg38]) JGAD000139: 1.36 TB (bam [ref: hg38]) |
| Comments (Policies) |
NBDC policy (JGAD000095, JGAD000122, JGAD000139) 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 MSI-H CRC (ICD10: C18, 19, 20): 94 cases CRC with liver metastasis: 12 cases, CRC without liver metastasis: 16 cases (ICD10: C18, 19, 20) |
| 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) |
breast cancer and lung adenocarcinoma: 103 bp MSI-H CRC: 104 bp or 135 bp CRC (JGAD000139): 133 bp |
| Japanese Genotype-phenotype Archive Data set ID |
Breast cancers: JGAD000095 Lung adenocarcinoma: JGAD000111 (fastq) MSI-H CRC: JGAD000122 (fastq) CRC: JGAD000139 (fastq) |
| Total Data Volume |
JGAD000095: 8.94 TB (fastq) JGAD000111: 1.31 TB (fastq) JGAD000122: 5.99 TB (fastq) JGAD000139: 1.91 TB (fastq) |
| Comments (Policies) |
NBDC policy (JGAD000095, JGAD000122, JGAD000139) NBDC policy & Company User Limit (JGAD000111) |
| Participants/Materials | MSI-H CRC (ICD10: C18, 19, 20): 18 cases |
| Targets | RNA access |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2000/2500] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq® RNA Access Library Prep Kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 104 bp or 135 bp |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000122 (fastq) |
| Total Data Volume | 5.99 TB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
MSI-H CRC (ICD10: C18, 19, 20): 93 cases normal tissues: 20 samples |
| Targets | Methylation array |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium Human MethylationEPIC BeadChip] |
| Source | DNAs extracted from tumor tissues and paired non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Infinium Human MethylationEPIC BeadChip Kit |
| Algorithms for Calculating Methylation-rate (software) | GenomeStudio (Illumina) |
| Filtering Methods | Detection P-value >= 0.05 |
| Normalization of microarray | - |
| Probe Number | 867,926 Probe Numbers |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000122 |
| Total Data Volume | 5.99 TB (tsv) |
| Comments (Policies) | NBDC policy |
| Participants/Materials: | MSI-H CRC (ICD10: C18, 19, 20): 25 cases |
| Targets | genome wide CNVs |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HumanOmni2.5-8 BeadChip] |
| Source | DNAs extracted from tumor tissues and paired non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Infinium HumanOmni2.5-8 kit |
| Algorithm for detecting CNVs (software) | GenomeStudio (Illumina) |
| Filtering Methods | As described in 'Illumine Infinium Assay Ver.2.1.' |
| CNV number | - |
| Japanese Genotype-phenotype Archive Data set ID | JGAD000122 |
| Total Data Volume | 5.99 TB (tsv) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hiroyuki Mano
Affiliation: Division of Cellular Signaling, National Cancer Center Research Institute
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, The Japan Agency for Medical Research and Development (AMED) | 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 | - |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Elucidation of initiation and progression mechanism of human epithelial tumors towards identification of novel therapeutic targets | JP17cm0106502 |
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 |
| 3 | Fusion Kinases Identified by Genomic Analyses of Sporadic Microsatellite Instability-High Colorectal Cancers | doi: 10.1158/1078-0432.CCR-18-1574 | JGAD000122 |
| 4 | Genomic profiles of colorectal carcinoma with liver metastases and newly identified fusion genes | doi: 10.1111/cas.14127 | JGAD000139 |
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 |
| Tetsuya Sato | Research Department, Miraca Research Institute G.K. | JGAD000095, JGAD000122 | 2019/08/05-2020/03/31 |
| Kouya Shiraishi | Division of Genome Biology, National Cancer Research Institute | JGAD000095, JGAD000110, JGAD000111, JGAD000122 | 2019/08/05-2023/03/31 |
| Ruping Sun | Department of laboratory medicine and pathology, University of Minnesota | JGAD000095 | 2020/03/19-2022/08/01 |
| Masaki Mandai | Kyoto University Faculty of Medicene, department of Gynecology and Obstetrics | JGAD000095, JGAD000110, JGAD000111, JGAD000122 | 2020/03/13-2025/03/31 |
