NBDC Research ID: hum0401.v3
SUMMARY
Aims: Sarcomas are classified as rare cancers, that is, cancers with an incidence of 6/100000 patients per year. The prognosis of rare cancers, including sarcomas, is poorer than that of common cancers because of the lack of effective treatment. One of the reasons is that the biological resources of sarcomas are not sufficient for advanced research. Therefore, we are establishing several types of sarcomas recapitulating biological characteristics of them including cell lines, organoids, and mouse models in order to develop effective novel treatment against sarcomas.
Methods: RNA sequencing, Whole-exome sequencing
Participants/Materials: giant cell tumor of bone: 1 case, chondrosarcoma: 2 cases, synovial sarcoma: 3 cases, histiocytic sarcoma: 1 case
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000618 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2023/06/29 |
| JGAS000834 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2025/10/27 |
| JGAS000806 | NGS (RNA-seq) | Controlled-access (Type I) | 2025/11/26 |
| JGAS000807 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2025/11/26 |
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MOLECULAR DATA
Exome (JGAS000618 / JGAS000834 / JGAS000807)
| Participants/Materials |
[JGAS000618] giant cell tumor of bone (ICD10: C419): 1 case tumor tissue (2nd operation): 1 sample tumor tissue (3rd operation): 1 sample organoid derived xenograft tumor: 1 sample [JGAS000834] chondrosarcoma (ICD10: C499): 2 cases tumor tissue: 1 sample organoid derived xenograft tumor: 1 sample total: 4 samples [JGAS000807] histiocytic sarcoma (ICD10: C499): 1 case tumor tissue: 1 sample normal muscle tissue: 1 sample organoid derived xenograft tumor: 1 sample |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000/X Plus] |
| Library Source | DNAs extracted from normal and tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
giant cell tumor of bone: JGAD000747 chondrosarcoma: JGAD000976 histiocytic sarcoma: JGAD000949 |
| Total Data Volume |
JGAD000747: 69.2 GB (fastq) JGAD000976: 47.9 GB (fastq) JGAD000949: 31.4 GB (fastq) |
| Comments (Policies) | NBDC policy |
RNA-seq (JGAS000618 / JGAS000806)
| Participants/Materials |
[JGAS000618] giant cell tumor of bone (ICD10: C419): 1 case normal muscle tissue: 1 sample tumor tissue (2nd operation): 1 sample tumor tissue (3rd operation): 1 sample patient derived organoid: 2 samples organoid derived xenograft tumor: 3 samples [JGAS000806] synovial sarcoma (ICD10: C499): 3 cases tumor tissue: 1 sample normal muscle tissue: 1 sample organoid derived xenograft tumor: 1 sample total: 9 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | MGI [DNBSEQ-G400/T7] |
| Library Source | RNAs extracted from normal and tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | MGIEasy RNA Directional Library Prep Set |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
giant cell tumor of bone: JGAD000747 synovial sarcoma: JGAD000948 |
| Total Data Volume |
JGAD000747: 69.2 GB (fastq) JGAD000948: 31.4 GB (fastq) |
| Comments (Policies) | NBDC policy |
RNA-seq (JGAS000834 / JGAS000807)
| Participants/Materials |
[JGAS000834] chondrosarcoma (ICD10: C499): 2 cases tumor tissue: 1 sample non-tumor tissue (muscle tissue): 1 sample organoid derived xenograft tumor: 1 sample total: 6 samples [JGAS000807] histiocytic sarcoma (ICD10: C499): 1 case tumor tissue: 1 sample normal muscle tissue: 1 sample organoid derived xenograft tumor: 2 samples total: 4 samples |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000/X Plus] |
| Library Source | RNAs extracted from normal and tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext® Ultra II Directional RNA Library Prep Kit |
| Fragmentation Methods | chemical fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
chondrosarcoma: JGAD000976 histiocytic sarcoma: JGAD000949 |
| Total Data Volume |
JGAD000976: 47.9 GB (fastq) JGAD000949: 31.4 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Toru Wakamatsu
Affiliation: Department of Musculoskeletal Oncology Service, Osaka International Cancer Institute
Project / Group Name: -
URL: https://oici.jp.e.abv.hp.transer.com/hospital/department/gansenmoni/seikei/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Early-Career Scientists | Development of sarcoma organoid panel for novel treatment | 20K18048 |
| KAKENHI Grant-in-Aid for Scientific Research (C) | Development of novel therapeutic strategies for sarcomas using patient-derived organoid models | 23K08600 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Genetic characterization of a novel organoid from human malignant giant-cell tumor | doi: 10.1016/j.jbo.2023.100486 | JGAD000747 |
| 2 | Chondrosarcoma Organoids Reveal Targetable SHH Pathway Activation via PTCH1 Alterations | JGAD000976 | |
| 3 | Development of synovial sarcoma organoids exhibiting ferroptosis resistance despite low malic enzyme 1 expression | JGAD000948 | |
| 4 | Establishment of human histiocytic sarcoma organoids dependent on the SHH/YAP pathway | doi: 10.1007/s13577-025-01308-6 | JGAD000949 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
