NBDC Research ID: hum0157.v1
SUMMARY
Aims: Cancer clinical sequence and accompanying research for comprehensive genomic and epigenomic analyses
Methods: DNA and RNA from tumor tissues (FFPE) and DNA from normal blood cells were subjected to target capture DNA panel sequencing and RNA panel sequencing by using of NextSeq (Illumina).
Participants/Materials: 183 cancer cases (lung cancer: 53, soft tissue sarcoma: 39, colon cancer: 24, endometrial cancer: 15, ovarian cancer: 12, endometrial sarcoma: 8, hypopharyngeal cancer: 4, adenoid cystic carcinoma: 4, cancer of unknown primary: 5, other types of cancer: 19)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000164 | NGS (Target Capture) | Controlled-access (Type I) | 2019/08/19 |
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MOLECULAR DATA
| Participants/Materials |
cancer: 183 cases (tumor tissues [FFPE sample] and normal blood cells) lung cancer (ICD10: C34): 53 cases soft tissue sarcoma (ICD10: C40-41): 39 cases colon cancer (ICD10: C17-20): 24 cases endometrial cancer (ICD10: C54): 15 cases ovarian cancer (ICD10: C56): 12 cases endometrial sarcoma (ICD10: C54): 8 cases hypopharyngeal cancer (ICD10: C13): 4 cases adenoid cystic carcinoma (ICD10: C07-08): 4 cases cancer of unknown primary (ICD10: D48): 5 cases other types of cancer: 19 cases |
| Targets | Target Capture |
| Target Loci for Capture Methods |
DNA panel: 464 genes RNA panel: 449 genes |
| Platform | Illumina [NextSeq] |
| Library Source | DNAs extracted from tumor tissues and peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | SureSelectXT Custom kit |
| Fragmentation Methods | Enzymatic fragmentation (Kapa Biosystems) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 151 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000242 |
| Total Data Volume | 3 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Kohei Miyazono
Affiliation: Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Program for an Integrated Database of Clinical and Genomic Information, Japan Agency for Medical Research and Development (AMED) | Establishment of infrastructure for genomic medicine and construction of knowledge database | JP18kk0205003 |
| Leading Advanced Projects for medical innovation, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-LEAP) | Project for Exploration of Cancer Therapeutic Targets | JP18am0001001 |
| 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. | JP18ck0106252 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Elucidation of initiation and progression mechanism of human epithelial tumors towards identification of novel therapeutic targets | JP18cm0106502 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Comprehensive assay for the molecular profiling of cancer by target enrichment from formalin-fixed paraffin-embedded specimens. | doi: 10.1111/cas.13968 | JGAD000242 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Hirofumi Nakaoka | Department of Cancer Genome Research, Sasaki Institute | Japan | Genetic analysis of lung cancer | JGAD000242 | 2022/08/06-2023/03/31 |
