NBDC Research ID: hum0376.v2
SUMMARY
Aims: To establish xenografts and cultured cell lines from clinical samples, as a bioresource for the development of a method of treatment, and to investigate their establishment methods.
Methods: A targeted sequencing analysis was performed using the NCC Oncopanel v4 test, which can analyze mutations of 114 genes and amplifications and fusions of 12 genes.
Participants/Materials: Endometrial cancer samples and their xenografts. Samples of one parent tissue and one xenograft each from two + four cases.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000585 | NGS (Target Capture) | Controlled-access (Type I) | 2022/12/27 |
| JGAS000585 (Data addition) | NGS (Target Capture) | Controlled-access (Type I) | 2023/03/28 |
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| Participants/Materials |
endometrial cancer (ICD10: C54.1) : 2 + 4 cases tumor tissue: 1 sample each patient-derived xenograft: 1 sample each |
| Targets | Target Capture |
| Target Loci for Capture Methods |
NCC Oncopanel v4 https://www.ncc.go.jp/en/information/press_release/20190717/20190717152024.html |
| Platform | Illumina [NextSeq 500] |
| Library Source | DNAs extracted from tumor tissues and xenograft samples |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect XT Reagents + KAPA Hyper Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | WA-MEM |
| Mapping Quality | ≥0 |
| Reference Genome Sequence | hg19 |
| Coverage (Depth) | 1240.7 (UXE009T-Fr2), 1119.6 (UXE009T2P8-Fr2), 1496.7 (UXE010T-Fr2), 1225.0 (UXE010T3P8-Fr2), 2039.1 (UXE001T-Fr1), 1952.7 (UXE001P8-Fr1), 2180.5 (UXE004T-Fr1), 2518.6 (UXE004P8-Fr1), 2141.6 (UXE005T-Fr1), 1830.4 (UXE005P8-Fr1), 2337.9 (UXE008T-Fr1), 2155.6 (UXE008P8-Fr1) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000712 |
| Total Data Volume | 4.5 + 16.9 GB (bam) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Toshio Imai
Affiliation: Department of Cancer Model Development, National Cancer Center Research Institute
Project / Group Name: -
URL: https://www.ncc.go.jp/en/ri/department/cancer_model_development/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| The National Cancer Center Research and Development Fund | Promotion of TR and drug discovery research by evolving and combining FIOC fore facility functions and bioresources | 2020J-002 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Alteration in molecular properties during establishment and passaging of endometrial carcinoma patient-derived xenografts | doi: 10.1038/s41598-023-35703-6 | JGAD000712 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
