NBDC Research ID: hum0120.v4
SUMMARY
Aims: To identify the biomarkers of predicting metastasis and recurrence in colorectal cancer (CRC), gastric cancer, and breast cancer.
Methods:
- DNAs and RNAs were extracted from the tumor and matched normal tissues. Whole exome sequencing was performed using tumor and matched normal tissues. RNA-seq, TCR repertoire, methylation array, and whole genome bisulfite sequencing analyses were performed using tumor tissues.
- Circulating tumor DNA were extracted from patients plasma and targeted sequence were performed.
Participants/Materials: 10 cases of stage 1 and 2 CRCs, which cases occurred liver or lung metastasis.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000221 | NGS (Exome) | Controlled-access (Type I) | 2020/04/03 |
| DRA011183 | NGS (Exome) | Unrestricted-access | 2020/04/03 |
| DRA011184 | NGS (RNA-seq) | Unrestricted-access | 2020/04/03 |
| DRA011185 | NGS (Target Capture) | Unrestricted-access | 2020/10/30 |
| E-GEAD-396 | Methylation array | Unrestricted-access | 2021/12/06 |
| DRA010902 | NGS (WGBS) | Unrestricted-access | 2021/12/06 |
| JGAS000549 | NGS (Target Capture) | Controlled-access (Type I) | 2022/07/29 |
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*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
MOLECULAR DATA
| Participants/Materials |
CRC (ICD10: C189): 10 cases (36 samples) - tumor tissues (colon: 10 samples, liver: 9 samples, lung: 5 samples) - non-tumor mucosa tissues (colon: 8 samples, lung: 4 samples) |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from tumor and matched non-tumor tissues from CRCs |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human ALL Exon V5 |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID / DDBJ Sequence Read Archive ID |
non-tumor tissues: JGAD000311 tumor tissues: DRA011183 |
| Total Data Volume | 414 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
CRC (ICD10: C189): 10 cases (20 samples) - primary tumor tissues: 8 samples - metastatic tumor tissues: 12 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor tissues from CRC |
| Cell Lines | - |
| Library Construction (kit name) | Agilent SureSelect Strand Specific RNA Kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| DDBJ Sequence Read Archive ID | DRA011184 |
| Total Data Volume | 414 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
CRC (ICD10: C189): 10 cases (20 samples) - primary tumor tissues: 8 samples - metastatic tumor tissues: 12 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods | T-cell receptor β chain region |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor tissues from CRC |
| Cell Lines | - |
| Library Construction (kit name) | KAPA HiFi HotStart Ready Mix PCR Kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| DDBJ Sequence Read Archive ID | DRA011185 |
| Total Data Volume | 16 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
CRC (ICD10: C189): 10 cases - circulating tumor DNA samples from patients' plasma: 77 samples (before/after radical surgery) |
| Targets | Target Capture |
| Target Loci for Capture Methods | 452 mutated genes commoned in primary tumor and metastatic tumor (mutated genes list) |
| Platform | Illumina [HiSeq 2500] |
| Library Source | Circulating tumor DNA extracted from CRC patients' plasma |
| Cell Lines | - |
| Library Construction (kit name) | SureSelectXT Custom 1kb-499kb (Agilent Technologies) |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 200 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000667 |
| Total Data Volume | 410.4 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
CRC (ICD10: C189): 16 cases gastric cancer (ICD10: C169): 16 cases breast cancer (ICD10: C509): 16 cases - primary tumor tissues: 16 samples each |
| Targets | Methylation array |
| Target Loci for Capture Methods | - |
| Platform | Illumina [iScan] |
| Source | DNAs extracted from tumor tissues from CRC, gastric cancer, and breast cance |
| Cell Lines | - |
| Reagents (Kit, Version) | Infinium MethylationEPIC Kit, v1.0 |
| Algorithms for Calculating Methylation-rate (software) | GenomeStudio Methylation Module v1.8 |
| Probe Number | 866,836 |
| Genomic Expression Archive Dataset ID | E-GEAD-396 |
| Total Data Volume | 1.3 GB (idat) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
CRC (ICD10: C189): 9 cases (18 samples) - primary tumor tissues: 9 samples - metastatic tumor tissues: 9 samples |
| Targets | WGBS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X Ten] |
| Library Source | DNAs extracted from tumor tissues from CRC |
| Cell Lines | - |
| Library Construction (kit name) | Miura F, et al.. Nucleic Acids Research (2019), 47, e85. |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| DDBJ Sequence Read Archive ID | DRA010902 |
| Total Data Volume | 1101 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Koshi Mimori
Affiliation: Department of Surgery, Kyushu University Beppu Hospital
Project / Group Name: -
URL: https://www.beppu.kyushu-u.ac.jp/gekareview/en/
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) | Understanding of molecular mechanisms to generate genetic heterogeneity associated with micro-environmental diversity for development of novel therapy and diagnostic technology in intractable cancers. | JP19cm0106504 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin. | doi: 10.1038/s41417-021-00401-w |
E-GEAD-396 DRA010902 |
| 2 |
USRES (Controlled-Access Data)
| Principal Investigator | Affiliation | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|
| Kouya Shiraishi | Division of Genome Biology, National Cancer Research Institute | Elucidation of immune-system networks between host and tumor based on genomic analysis | JGAD000311 | 2019/09/18-2023/03/31 |
