NBDC Research ID: hum0355.v1
SUMMARY
Aims: To investigate genetic (variants, copy number alterations, structural abnormalities, etc.), epigenetic, and transcriptomic profiles of genitourinary tumors (adrenal, kidney, renal pelvis, retroperitoneal, ureter, ureteric duct, bladder, prostate, urethra, penis, testis, etc.). At the same time, by combining the profiles with clinical data (patient's background, treatment outcome, and prognosis), we clarify the relationship between the profiles and therapeutic efficacy, and molecular pathogenesis.
Methods: whole-genome sequencing (NGS), whole-exome sequencing (NGS), RNA-sequence (NGS), and digital multiplexed gene expression analysis using the NanoString nCounter system
Participants/Materials: Ten patients with hereditary clear cell renal cell carcinoma (ccRCC) associated with Von Hippel-Lindau (VHL) disease
URL: https://www.ncc.go.jp/en/ri/division/molecular_oncology/index.html
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000544 | Controlled-access (Type I) | 2023/06/19 |
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MOLECULAR DATA
| Participants/Materials |
hereditary ccRCC (ICD10: C64) with VHL (ICD10: Q858): 1 case peripheral blood: 1 sample (for germline VHL gene alteration testing) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Library Source | DNAs extracted from peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Nano DNA Library Prep Kit |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | bwa |
| Mapping Quality | 10x coverage width: 99% |
| Reference Genome Sequence | hs37d5 |
| Coverage (Depth) | 34X |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000663 |
| Total Data Volume | 1.1 TB (bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hereditary ccRCC (ICD10: C64) with VHL (ICD10: Q858): 10 cases (98 samples) primary tumor: 10 cases (81 samples) metastatic tumor: 1 case (7 samples [1 lung, 3pleura, and 3 lymph nodes]) peripheral blood: 10 cases (10 samples) |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NextSeq 500, NovaSeq 6000] |
| Library Source | DNAs extracted from tumor tissues and peripheral blood cells |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6, SureSelectXT HS Target Enrichment System, SureSelectXT Target Enrichment System |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | bwa |
| Mapping Quality | Median 30x coverage width: 97% |
| Reference Genome Sequence | hs37d5 |
| Coverage (Depth) | 166X |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000663 |
| Total Data Volume | 1.1 TB (bam) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
hereditary ccRCC (ICD10: C64) with VHL (ICD10: Q858): 7 cases (49 samples) primary tumor: 7 cases (49 samples) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq X Ten] |
| Library Source | RNAs extracted from tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Ultra II RNA Library Prep Kit for Illumina |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 150 bp |
| Mapping Methods | bwa |
| Mapping Quality | Median mapped reads 9,639,928 |
| Reference Genome Sequence | hs37d5 |
| Gene number | 26,718 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000663 |
| Total Data Volume | 1.1 TB (bam) |
| Comments (Policies) | NBDC policy |
Digital multiplexed gene expression analysis
| Participants/Materials |
hereditary ccRCC (ICD10: C64) with VHL (ICD10: Q858): 9 cases (82 samples) primary tumor: 9 cases (76 samples) normal renal cortex: 6 cases (6 samples) |
| Targets | Direct Digital Count |
| Target Loci for Capture Methods | 594 genes |
| Platform |
Chip: nCounter Human Immunology V2 panel Scanner: NanoString Technologies [nCounter Digital Analyzer] |
| Source | RNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Reagents (Kit, Version) | nCounter Human Immunology V2 Panel CodeSet |
| Software | nSolver analysis software v4.0.70 |
| Filtering Methods (normalization, QC) | nSolver analysis software v4.0.70 |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000663 |
| Total Data Volume | 1.1 TB (txt) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Keisuke Kataoka
Affiliation: Division of Molecular Oncology, National Cancer Center Research Institute
Project / Group Name: -
URL: https://www.ncc.go.jp/en/ri/division/molecular_oncology/index.html
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Project for Promotion of Cancer Research and Therapeutic Evolution (P-PROMOTE), Japan Agency for Medical Research and Development (AMED) | Elucidation of inter-patient, inter-tumor, and intra-tumor heterogeneity of genetic and immune status | JP23ama221510 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Inter- and intra-tumor heterogeneity of genetic and immune profiles in inherited renal cell carcinoma | doi: 10.1016/j.celrep.2023.112736 | JGAD000663 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Maher Eamonn | University of Cambridge | United Kingdom of Great Britain and Northern Ireland | Molecular Pathology of Human Genetic Disease | JGAD000663 | 2023/03/19-2024/07/20 |
