NBDC Research ID: hum0301.v1
SUMMARY
Aims: To clarify the relationship between genomic abnormalities and immune status in cancer patients and high-risk individuals, we analyzed various immunocompetent cells/factors (immunological profile) in tumor tissues, normal mammary tissue, and peripheral blood cells for genetic mutations. The relationship between immune status and clinicopathological/biological features, treatment response, and prognosis were examined as a secondary endpoint.
Methods: For target sequence, genomic DNA was extracted using QIAamp DNA Mini Kits or QIAamp Fast DNA Tissue Kit for fresh-frozen samples and GeneRead DNA FFPE Kit for formalin-fixed-paraffin-embedded (FFPE) samples.
Participants/Materials: Tumor tissues and normal breast tissues from 26 patients with breast cancer (fresh frozen samples and FFPE samples)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000368 | NGS (Target Capture) | Controlled-access (Type I) | 2021/11/29 |
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| Participants/Materials |
breast cancer (ICD10: C50.9): 26 cases (Total: 329 samples) fresh-frozen tumor tissue: 9 cases, 23 samples FFPE tumor tissue: 19 cases, 37 samples fresh-frozen normal breast tissue: 14 cases, 57 samples FFPE normal breast tissue: 22 cases, 212 samples |
| Targets | Target Capture |
| Target Loci for Capture Methods | 464 genes (Todai OncoPanel, a custom target-capturing panel) |
| Platform |
Illumina [HiSeq 2500, NovaSeq 6000] MGI Technologies [DNBSEQ-G400] |
| Library Source | DNAs extracted from tumor tissues and normal breast tissues (fresh-frozen and FFPE samples) |
| Cell Lines | - |
| Library Construction (kit name) |
Illumina: SureSelectXT Custom kits [Agilent Technologies] or Twist Custom Panels [Twist Bioscience] MGI: DNA libraries for Illumina sequencer were converted to single-stranded circular DNA libraries for MGI sequencer with the MGIEasy Universal Library Conversion Kit [MGI Technologies] |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 124–151 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000482 |
| Total Data Volume | 814.2 GB (bam [ref: hg38]) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hiroyuki Mano
Affiliation: Division of Cellular Signaling, National Cancer Center Research Institute
Project / Group Name: Immuno-Genome Atlas Project (iGAP)
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Implementation of precision medicine by the application of an innovative method for functional evaluation of oncogenes. | JP19ck0106252 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | MicroSEC filters sequence errors for formalin-fixed and paraffin-embedded samples | doi: 10.1038/s42003-021-02930-4 | JGAD000482 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
