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 IDType of DataCriteriaRelease Date
JGAS000177 NGS (Exome, RNA-seq, Target Capture) Controlled-access (Type I) 2019/09/20

*Release Note  

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MOLECULAR DATA

Exome

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

 

RNA-seq

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

 

Target Capture

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):

NameTitleProject 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

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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