NBDC Research ID: hum0301.v1



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 IDType of DataCriteriaRelease Date
JGAS000368 NGS (Target Capture) Controlled-access (Type I) 2021/11/29

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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)

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



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):

NameTitleProject 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



TitleDOIDataset ID
1 MicroSEC filters sequence errors for formalin-fixed and paraffin-embedded samples doi: 10.1038/s42003-021-02930-4 JGAD000482


USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use