NBDC Research ID: hum0385.v2
SUMMARY
Aims: To investigate genetic mutations of Combined hepatocellular-cholangiocarcinoma, Cholangiolocarcinoma, Keratin 19-expressing hepatocellular carcinoma, and SOX9-expressing hepatocellular carcinoma and to clarify their association with clinicopathological features
Methods: We obtained non-tumor and tumor tissues from surgical specimens of cholangiolocarcinoma and combined hepatocellular-cholangiocarcinoma and extracted DNA from tissues, then performed whole-exome sequencing analysis.
Participants/Materials: Cholangiolocarcinoma and combined hepatocellular-cholangiocarcinoma patients
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000597 | NGS (Exome) | Controlled-access (Type I) | 2023/12/14 |
| JGAS000599 | NGS (Exome) | Controlled-access (Type I) | 2024/01/09 |
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MOLECULAR DATA
| Participants/Materials |
cholangiolocarcinoma (ICD10: C221): 8 cases tumor tissue: 8 samples, non-tumor tissue: 8 samples, recurrent tumor tissue: 2 samples combined hepatocellular-cholangiocarcinoma (ICD10: 227): 13 cases tumor tissue: 13 samples, non-tumor tissue: 13 samples, recurrent tumor tissue: 2 samples |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris LE220) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
cholangiolocarcinoma: JGAD000726 combined hepatocellular-cholangiocarcinoma: JGAD000728 |
| Total Data Volume |
JGAD000726: 157.1 GB (fastq) JGAD000728: 169.3 GB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Takamichi Ishii
Affiliation: Department of Surgery, Graduate School of Medicine, Kyoto University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Elucidation of Genomic Heterogeneity in Hepatocellular Carcinoma from the Perspective of Cancer Stem Cells | 19K09145 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Integrated analyses of the genetic and clinicopathological features of cholangiolocarcinoma: cholangiolocarcinoma may be characterized by mismatch-repair deficiency. | doi:10.1002/path.6257 | JGAD000726 |
| 2 | Comprehensive analyses of the clinicopathological features and genomic mutations of combined hepatocellular-cholangiocarcinoma | doi: 10.1111/hepr.13965 | JGAD000728 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
