NBDC Research ID: hum0233.v1
SUMMARY
Aims: To characterize the genomic profile of hepatoblastoma and hepatocellular carcinoma and then to compare these data to clinical course of the patients for development of novel treatment strategies accoding to tumor biological characteristics
Methods: Whole Exome Sequencing (NGS), RNA-seq (NGS), SNP array, Methylation array, Whole Genome Bisulfite Sequencing (NGS)
Participants/Materials: 165 clinical hepatoblastoma samples
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000236 | Controlled-access (Type I) | 2021/05/31 |
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MOLECULAR DATA
| Participants/Materials |
Pediatric hepatoblastoma (ICD10: C22.0, C22.2): 112 cases tumor tissue: 112 samples non-tumor tissue: 112 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from tumor tissues and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect XT Exome V5 Custom kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris S2) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| QC | - |
| Mapping Methods | BWA, Karkinos (in-house mapper) |
| Coverage (Depth) | - |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000334 |
| Total Data Volume | 2 TB (bam [ref: hg19]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pediatric hepatoblastoma (ICD10: C22.0, C22.2): 113 cases tumor tissue: 111 samples non-tumor tissue: 28 samples (tumor and matched-non tumor pair: 26 cases + tumor tissues only: 85 cases + non-tumor tissues only: 2 cases) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor tissues and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq RNA LT Sample Prep Kit |
| Fragmentation Methods | included in the above library construction kit |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| QC | - |
| Mapping Methods | BWA, Finemap (in-house mapper) |
| Coverage (Depth) | - |
| Total Reads / Uniquely Mapped Reads | - |
| Gene Numbers | 86,817 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000334 |
| Total Data Volume | 2 TB (bam [ref: hg19], FPKM [txt]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pediatric hepatoblastoma (ICD10: C22.0, C22.2): 112 cases tumor tissue: 112 samples non-tumor tissue: 112 samples |
| Targets | genome wide SNPs |
| Target Loci for Capture Methods | - |
| Platform | Affymetrix [Genome-Wide Human SNP Array 6.0] |
| Source | DNAs extracted from tumor tissues and non-tumor tissues |
| Cell Lines | - |
| Reagents (Kit, Version) | Affymetrix Genome-Wide Human SNP Assay Kit 6.0 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000334 |
| Total Data Volume | 2 TB (CEL) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pediatric hepatoblastoma (ICD10: C22.0, C22.2): 146 cases tumor tissue: 146 samples non-tumor tissue: 32 samples (tumor and matched-non tumor pair: 32 cases + tumor tissues only: 114 cases + non-tumor tissues only: 0 case) |
| Targets | Methylation array |
| Target Loci for Capture Methods | - |
| Platform | Illumina [Infinium Human Methylation 450K BeadChip] |
| Library Source | DNAs extracted from tumor tissues and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Infinium HumanMethylation450 BeadChip |
| Algorithms for Calculating Methylation-rate (software) | Genome Studio |
| Filtering Methods | - |
| Normalization of microarray | following the standard protocol of Genome Studio |
| Probe Number | 485,577 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000334 |
| Total Data Volume | 2 TB (beta value [txt, ref: hg19]) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
Pediatric hepatoblastoma (ICD10: C22.0, C22.2): 21 cases tumor tissue: 20 samples non-tumor tissue: 3 samples (tumor and matched-non tumor pair: 2 cases + tumor tissues only: 18 cases + non-tumor tissues only: 1 case) |
| Targets | WGBS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | DNAs extracted from tumor tissues and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | EZ DNA Methylation-Gold |
| Fragmentation Methods | fragmentation due to bisulfite conversion |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100 bp |
| QC | high mapping efficiency (58.3%) |
| Mapping Methods | Bowtie2 v2.2.5 (Bismark v0.14.3) |
| Coverage (Depth) | 19.7X |
| Total Reads / Uniquely Mapped Reads | Total reads: 627,297,250 (mean) / Uniquely mapped reads: 364,372,627 (mean) |
| Detecting Methods for Variation | Bismark (v0.14.3) |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000334 |
| Total Data Volume | 2 TB (bigwig [ref: hg19]) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Eiso Hiyama
Affiliation: Natural Science Center for Basic Research and Development, Hiroshima University
Project / Group Name: JPLT-2 project / Japanese study group for Pediatric Liver Tumor (JPLT)
URL: https://home.hiroshima-u.ac.jp/eiso/english/home.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Development of standard treatments for childhood embryonal solid tumors | JP18CK0106332 |
| Project Promoting Clinical Trials for Development of New Drugs, Japan Agency for Medical Research and Development (AMED) | Clinical international collaboration trials for drug development in childhood liver tumors under the nationwide childhood cancer registry | JP18LK0201066 |
| Project for Cancer Research and Therapeutic Evolution (P-CREATE), Japan Agency for Medical Research and Development (AMED) | Elucidation of initiation and progression mechanism of human epithelial tumors towards identification of novel therapeutic targets | JP19cm0106502 |
| Tailor-Made Medical Treatment with the BioBank Japan Project (BBJ), Japan Agency for Medical Research and Development (AMED) | Establishment of a Biobank and Creation of a Database of Clinical Information | JP16km0305001 |
| Practical Research for Innovative Cancer Control, Japan Agency for Medical Research and Development (AMED) | Identification of new diagnostic biomarkers and development of new therapeutic strategies in intractable childhood malignant solid tumors | JP16ck0106070 |
| KAKENHI Grant-in-Aid for Scientific Research (A) | Cancer fluid biopsy for childhood malignancies using one cell analysis | 15H02567 |
| KAKENHI Grant-in-Aid for Scientific Research (A) | Study of clinical states and infrastructure development of International co-operative clinical trial for childhood liver tumors by children's cancer study group | 16H02778 |
| KAKENHI Grant-in-Aid for Scientific Research (A) | Next-generation cancer liquid biopsy of childhood cancers using single cell analysis | 19H01056 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Jinyan Huang | School of Medicine, Zhejiang University | Comprehensive analysis of alternative splicing in malignant tumors | JGAD000334 | 2022/03/07-2024/01/01 | |
| Tianzhong Yang | Childhood Cancer Genomic Group, Division of Biostatistics, University of Minnesota | United States of America | Evaluating germline genetic risk factors of hepatoblastoma onset and survival | JGAD000334 | 2022/09/19-2025/08/27 |
| Michiaki Hamada | Faculty of Science and Engineering, Waseda University | Japan | Construction of RNA-targeted Drug Discovery Database | JGAD000334 | 2022/12/26-2025/03/31 |
| Yujie Tang | Department of Histoembryology, Genetics and Developmental Biology, College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine | China | The key molecular mechanisms underlying the oncogenesis and progression of neuroblastoma and hepatoblastoma | JGAD000334 | 2023/03/07-2027/12/31 |
| Xin Chen | University of Hawaii Cancer Center | United States of America | Wnt/beta-Catenin or Hippo/YAP target gene expression in hepatoblastoma | JGAD000334 | 2023/04/25-2026/03/31 |
| Weng Chuan Peng | Princess Maxima Center for Pediatric Oncology | Netherlands | Towards understanding pediatric liver tumors | JGAD000334 | 2023/08/22-2027/06/01 |
| Hiroki Hirao | Department of Pediatric Surgery and Transplantation, Kumamoto University Graduate School of Medical Sciences | Japan | SOX9 expression analysis in Hepatoblastoma | JGAD000334 | 2024/04/16-2026/03/31 |
