Skip to content
NBDC Human Database

No datasets in the cart.

Go to the cart

Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Research ID

hum0268-v2Release info

Latest

Research title

Direct and comprehensive identification of neoantigens using cancer tissues

Research overview

Aims
Proteogenomic discovery of a novel class of cancer antigens by HLA ligandome analysis of colon cancer tissues
Methods
[Human colon cancer cell line, colon cancer] RNA-seq, CAGE-seq and Iso-seq data were used to analyze the transcript variants coding an identified non-coding RNA-derived antigen.
[Endometrial cancer] Bulk RNA-seq of tumor tissues was used to comprehensively analyze the set of genes expressed in each tissue sample. WES of tumor tissue and peripheral blood detected somatic mutations in each case and was combined with HLA ligandome analysis using mass spectrometry to identify neoantigens. Single-cell RNA-seq/TCR-seq of tumor-infiltrating T cells was used to identify tumor-reactive cytotoxic CD4+ T cells and marker genes.
Participants/materials
Human colon cancer cell line: 1, colon cancer: 6 cases, endometrial cancer: 5 cases
URL
N/A

Datasets

CartDataset IDType of dataAnalysis methodAccess criteriaDate published
JGAD000386NGS (Iso-seq, CAGE-seq, RNA-seq)
  • Iso-seq
  • CAGE-seq
  • RNA-seq
Controlled-access (Type I)2021-04-09
JGAD000907NGS (RNA-seq, scRNA-seq, scTCR-seq, Exome)
  • RNA-seq
  • scRNA-seq
  • scTCR-seq
  • WES
Controlled-access (Type I)2025-08-29

Data provider

Principal investigator
Takayuki Kanaseki
Affiliation
Department of Pathology, Sapporo Medical University/Division of Molecular Pathology, Niigata University School of Medicine

Research projects

No research projects.

Grants

NameTitleProject number
Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED)
Proteogenomic discovery of HLA presented tumor antigens that arise from non-coding RNAs
  • JP20cm0106352
Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED)
Multiomics study of tumor-specific antigens and reactive T cells based on NAP proteogenomics
  • JP24ama221315
KAKENHI Grant-in-Aid for Scientific Research (B)
Functional Analysis of Tumor-Specific CD4+ T Cells Using a Novel Neoantigen Detection Technology
  • 24K02252

Related publications

TitleDOIDataset ID
CD8+ T-cell Immune Surveillance against a Tumor Antigen Encoded by the Oncogenic Long Noncoding RNA PVT1
https://doi.org/10.1158/2326-6066.CIR-20-0964 (opens in a new tab)
Identification and Phenotypic Characterization of Neoantigen-Specific Cytotoxic CD4+ T Cells in Endometrial Cancer
https://doi.org/10.1158/2326-6066.CIR-24-0514 (opens in a new tab)

Controlled access users

Principal investigatorAffiliationCountry/RegionResearch titlePeriod of data useDataset ID
Michiaki HamadaHamada Laboratory, Faculty of Science and Engineering, Waseda UniversityJapanConstruction of RNA-targeted Drug Discovery Database2023-01-05 – 2027-10-31