NBDC Research ID: hum0152.v2
SUMMARY
Aims: Analysis of genomic alterations in dedifferentiated liposarcoma
Methods: Exome sequencing, RNA sequencing, Whole genome sequencing
Participants/Materials: 37 patients with dedifferentiated liposarcoma, a patient with lipoblastoma-like tumor of the vulva (LLTV)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000182 | NGS (Exome, RNA-seq) | Controlled-access (Type I) | 2019/09/20 |
| JGAS000529 | NGS (WGS, Exome, RNA-seq) | Controlled-access (Type I) | 2022/11/15 |
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MOLECULAR DATA
| Participants/Materials | Dedifferentiated liposarcoma (ICD10: C480, C490, C492, C493): 37 cases |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Agilent SureSelect XT Human All Exon V5 |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000264 |
| Total Data Volume | 880 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | Dedifferentiated liposarcoma (ICD10: C480, C490, C492, C493): 37 cases |
| 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) | Ribo-Zero Gold kit |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 75 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000264 |
| Total Data Volume | 880 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | LLTV (ICD10: C49、C51): 1 case |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNA extracted from tumor tissue and blood |
| Cell Lines | - |
| Library Construction (kit name) | Twist Library Preparation EF kit |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | BWA-MEM |
| Mapping Quality | MAPQ < 20 were excluded |
| Reference Genome Sequence | hg38 |
| Coverage (Depth) | 81 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000648 |
| Total Data Volume | 233.6 GB (bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | LLTV (ICD10: C49、C51): 1 case |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNA extracted from tumor tissue and blood |
| Cell Lines | - |
| Library Construction (kit name) | Twist Library Preparation EF kit, Twist Comprehensive Exome Panel |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | BWA-MEM |
| Mapping Quality | MAPQ < 20 were excluded |
| Reference Genome Sequence | hg38 |
| Coverage (Depth) | 431 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000648 |
| Total Data Volume | 233.6 GB (bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials | LLTV (ICD10: C49、C51): 1 case |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | RNA extracted from tumor tissue |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra Directional RNA Library Prep Kit for Illumina |
| Fragmentation Methods | Enzymatic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000648 |
| Total Data Volume | 233.6 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hitoshi Ichikawa
Affiliation: Department of Clinical Genomics, National Cancer Center Research Institute
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Fundamental study for re-purposing of molecular targeting drugs for sarcoma using multi-omics approach | JP16ck0106089 |
| National Cancer Center Research and Development Funds | - | 26-A-1 |
| National Cancer Center Research and Development Funds | - | 26-A-1 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Frequent amplification of receptor tyrosine kinase genes in well-differentiated/ dedifferentiated liposarcoma | doi: 10.18632/oncotarget.14652 | JGAD000264 |
| 2 | Comprehensive genetic analysis of a lipoblastoma-like tumor of the vulva | doi: 10.1016/j.joscr.2022.09.002 | JGAD000648 |
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 | JGAD000264 | 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 | JGAD000264 | 2022/11/09-2024/10/01 |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000264 | 2022/12/26-2025/03/31 |
