NBDC Research ID: hum0153.v1
SUMMARY
Aims: Identification of genetics alterations of dedifferentiated liposarcoma and tendon sheath giant cell tumors (TSGCT)
Methods: DNAs and RNAs were extracted from tumor and paired non-tumor tissues (peripheral blood or adjacent normal tissues). Whole exome sequencing (WES), RNA sequencing, and target capture sequencing were performed by HiSeq 2500 or MiSeq (Illumina).
Participants/Materials: 29 dedifferentiated liposarcoma and 36 TSGCT patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000177 | NGS (Exome, RNA-seq, Target Capture) | Controlled-access (Type I) | 2019/09/20 |
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MOLECULAR DATA
| Participants/Materials |
Dedifferentiated liposarcoma (ICD10: C49): 29 cases - 29 dedifferentiated components, 8 well-differentiated components, and 29 peripheral blood tissues TSGCT (ICD10: D21): 10 cases - 10 tumor tissues and 10 non-tumor tissues |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from tumor and non-tumor tissues/peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) |
Dedifferentiated liposarcoma: SureSelect XT Human All Exon V5 + IncRNA kit TSGCT: SureSelect Exome V5 kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
Dedifferentiated liposarcoma: JGAD000257 TSGCT: JGAD000258 |
| Total Data Volume | 1 TB (bam, fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Dedifferentiated liposarcoma (ICD10: C49): 19 cases - 19 Dedifferentiated components and 7 well-differentiated components TSGCT (ICD10: C49): 18 cases - 18 tumor tissues |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA Prep kit or TruSeq RNA Access Library Prep kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 126 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
Dedifferentiated liposarcoma: JGAD000257 TSGCT: JGAD000258 |
| Total Data Volume | 1 TB (bam, fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
TSGCT (ICD10: C49): 34 cases - 34 tumor tissues and 34 non-tumorl tissues |
| Targets | Target Capture |
| Target Loci for Capture Methods | exon regions of CBL gene |
| Platform | Illumina [MiSeq] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | PCR + TruSeq Nano DNA Library Prepkit |
| Fragmentation Methods | - |
| Spot Type | Paired-end or Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000258 |
| Total Data Volume | 1 TB (bam, fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Koichi Matsuda / Makoto Hirata
Affiliation: Graduate school of Frontier Science / Institute of Medical Science, The University of Tokyo
Project / Group Name: Japan Sarcome genome consortium
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Genomic analysis of bone and soft tissue tumors and screening of their therapeutic targets and biomarkers | JP17cm0106520 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Genomic analysis of bone and soft tissue tumors and screening of their therapeutic targets and biomarkers | JP18cm0106535 |
| Project for Development of Innovative Research on Cancer Therapeutics (P-DIRECT), Japan Agency for Medical Research and Development (AMED) | Identification of novel therapeutic target of soft tissue tumors by genomic analysis. | JP15cm0106141 |
| KAKENHI Grant-in-Aid for Scientific Research (A) | Analysis of fusion transcripts in bone and soft tissue tumors for indentification of novel disease biomarker and reorganization of disease classification. | 16H02676 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Massively parallel sequencing of tenosynovial giant cell tumors reveals novel CSF1 fusion transcripts and novel somatic CBL mutations | doi: 10.1002/ijc.32421 |
JGAD000257 JGAD000258 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Valerie Brunton | Edinburgh Cancer Research UK Centrer | Genomic analysis of soft tissue sarcoma | JGAD000257, JGAD000258 | 2021/07/09-2024/02/29 | |
| William Tapper | Human Development and Health, University of Southampton | United Kingdom of Great Britain and Northern Ireland | Utilising sarcoma omic information to identify disease gene networks and associated novel therapies for patients | JGAD000257 | 2022/11/09-2024/10/01 |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000257, JGAD000258 | 2022/12/26-2025/03/31 |
