NBDC Research ID: hum0548.v1
SUMMARY
Aims: This study used about 2,000 cancer tissue samples and clinical data from Bioresource Research Center, Tokyo Medical and Dental University. Using the ACTOnco®+ panel targeting 440 genes, genomic analysis were integrated with clinical information to develop new diagnostics, therapies, and preventive strategies for personalized cancer medicine.
Methods: Target capture sequencing, RNA sequencing
Participants/Materials: 1,996 adult solid tumor patients who provided broad consent to the Biobank Project of Tokyo Medical and Dental University.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000863 | NGS (Target Capture, RNA-seq) | Controlled-access (Type I) | 2026/02/04 |
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MOLECULAR DATA
JGAS000863 (Target Capture, RNA-seq)
| Participants/Materials |
adult solid tumor (ICD10: C162, C169, C163, C160, C158, C161, C221, C251, C254, C220, C253, C250, D377, C240, C252, C787, C182, D137, C480, C788, C19, C170, C20, C23, C241, D376, D372, C171, J690, C187, C258, C64, C259, C248, C060, C029, C030, C031, C439, D480, C049, C062, C310, D370, C091, C050, C081, C080, D165, C151, C150, C159, C155, C153, C152, C12, C021, C040, C312, C01, C131, C73, C321, C300, C07, C041, D385, C311, D355, C490, C020, C102, C320, H618, C186, C189, C184, C180, C211, C181, C504, C505, C509, C500, C502, C503, C569, C501, D486, C508, C341, C343, C450, D487, C349, C342, C80, C33, D383, C629, C66, C675, D401, D350, C61, C541, C539, C56, C549, C482, C542, C530): 1,996 cases tumor tissues (FFPE samples): 1,996 samples |
| Targets | Target Capture, RNA-seq |
| Target Loci for Capture Methods | ACTOnco Comprehensive 440-Gene Cancer Panel (440 genes + 31 fusion genes) |
| Platform | Life Technologies [Ion Proton] |
| Library Source | DNAs/RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Ion AmpliSeq Library Kit (Thermo Fisher Scientific) |
| Fragmentation Methods | Amplicon PCR |
| Spot Type |
[DNA] Single-end [RNA] ACT SOP protocol |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | [RNA] ACT SOP protocol |
| Mapping Methods |
[DNA] Ion Torrent Suite [RNA] ACT SOP protocol |
| Mapping Quality |
[DNA] Not specified (variant-level coverage filtering applied) [RNA] ACT SOP protocol |
| Reference Genome Sequence |
[DNA] GRCh37 (hg19) [RNA] ACT SOP protocol |
| Coverage (Depth) |
[DNA] NGS Sequencing Mean Depth ≥ 500x [RNA] Total depth ≥ 20,000x RNA process controls ≥ 6 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD001006 |
| Total Data Volume | 435.5 KB (summary-level data; xlsx) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Toshihiro Tanaka
Affiliation: Department of Human Genetics and Disease Diversity, Institute of Science Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genomic landscape of oral squamous cell carcinoma highlights prognostic significance of NOTCH1 mutations and subsite-specific differences | JGAD001006 | |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
