NBDC Research ID: hum0277.v3
SUMMARY
Aims: To clarify the oncogenesis and the progression mechanism of urological tumors, we continuously collect tumor samples of our patients with high quality. Then we used them to comprehensive analyses such as genome sequencing or epi-genome sequencing. Through these analyses, we aim for elucidating the oncogenesis or for developing newly treatment strategies of each cancer.
Methods: single-cell RNA sequencing (scRNA-seq), whole exome sequencing (WES), RNA-seq, and Whole genome sequencing (WGS)
- scRNA-seq: We sliced surgically resected specimens and minced and digested into the single cell level. Libraries were prepared using Chromium single cell 3’ kit (10X Genomics) according to the manufacturer’s protocol. Paired-end sequencing was conducted on the NextSeq 500 platform (Illumina).
- WES: Libraries were prepared using SureSelect Human All Exon V6 (Agilent Technologies) and sequenced by using of NovaSeq 6000/PE150 (Illumina).
- RNA-seq: Libraries were prepared using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA CD Index Kit (Dual Index) and sequenced by using of HiSeq 2500 (Illumina).
- WGS: Genomic DNAs were extracted from frozen tissues. The library construction was done using the TruSeq Nano DNA Library Prep Kit and sequenced by using of NovaSeq 6000 (Illumina).
Participants/Materials: 19 patients with Birt-Hogg-Dubé (BHD) associated renal cell carcinoma (RCC), 1 patient with hereditary leiomyomatosis and renal cell cancer (HLRCC) associated RCC, 2 patients with Von Hippel-Lindau (VHL) associated RCC, 2 patients with sporadic clear cell RCC (ccRCC), 21 patients with sporadic chromophobe RCC (chRCC), and 7 patients with sporadic oncocytoma
- scRNA-seq: 2 BHD-associated RCC, 1 HLRCC-associated RCC, 2 VHL-associated RCC, and 2 ccRCC
- WES: 2 BHD-associated RCC, 1 HLRCC-associated RCC, 2 VHL-associated RCC, and 2 ccRCC
- RNA-seq: 10 BHD-associated RCC, 21 chRCC, and 7 sporadic oncocytoma
- WGS: 9 BHD-associated RCC
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000303 | NGS (scRNA-seq, Exome, RNA-seq) | Controlled-access (Type I) | 2022/09/09 |
| JGAS000564 | NGS (WGS, RNA-seq) | Controlled-access (Type I) | 2023/04/18 |
| JGAS000564 (Data addition) | NGS (RNA-seq) | Controlled-access (Type I) | 2023/05/10 |
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MOLECULAR DATA
| Participants/Materials |
RCC (ICD10: C64): 7 cases BHD (ICD10: Q878) -associated RCC: 2 cases (2 samples) HLRCC (MedGen ID: 353771) -associated RCC: 1 case (2 samples) VHL (ICD10: Q858) -associated RCC: 2 cases (2 samples) ccRCC: 2 cases (4 tumor samples and 2 normal kidney tissues) |
| Targets | scRNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000/NextSeq 500] |
| Library Source | RNAs extracted from single cells of tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Chromium single cell 3’ kit (10XGenomics) |
| Fragmentation Methods | - |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | index 8 bp, read1 28 bp, read2 91 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000414 |
| Total Data Volume | 316.9 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
RCC (ICD10: C64): 7 cases BHD (ICD10: Q878) -associated RCC: 2 cases (tumor: 2 samples, normal kidney: 2 samples) HLRCC (MedGen ID: 353771) -associated RCC: 1 case (tumor: 2 samples, normal kidney: 1 sample) VHL (ICD10: Q858) -associated RCC: 2 cases (tumor: 2 samples, normal kidney: 2 samples) ccRCC: 2 cases (tumor: 4 samples, normal kidney: 2 samples) |
| Targets | Exome |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000/PE150] |
| Library Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SureSelect Human All Exon V6 (Agilent Technologies) |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | read1 150 bp, read2 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000414 |
| Total Data Volume | 316.9 GB (fastq) |
| Comments (Policies) | NBDC policy |
RNA-seq (JGAS000303, JGAS000564)
| Participants/Materials |
BHD (ICD10: Q878) -associated RCC (ICD10: C64): 10 cases (tumor: 16 samples, normal kidney: 5 samples) chRCC (ICD10: C64): 21 cases (tumor: 21 samples) sporadic oncocytoma (ICD10: C64): 7 cases (tumor: 7 samples) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [HiSeq 2500] |
| Library Source | RNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | TruSeq Stranded mRNA Library Prep Kit, TruSeq RNA CD Index Kit (Dual Index) |
| Fragmentation Methods | Heat treatment |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | read1 126 bp, read2 126 bp |
| Japanese Genotype-phenotype Archive Dataset ID |
BHD-associated RCC: JGAD000414 chRCC and sporadic oncocytoma: JGAD000686 |
| Total Data Volume |
JGAD000414: 316.9 GB (fastq) JGAD000686: 1.4 TB + 20 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
BHD (ICD10: Q878) -associated RCC (ICD10: C64): 9 cases (tumor: 16 samples, normal kidney: 9 samples) |
| Targets | WGS |
| 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) | TruSeq Nano DNA Library Prep Kit (Illumina) |
| Fragmentation Methods | Ultrasonic fragmentation |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | read1 150 bp, read2 150 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000686 |
| Total Data Volume | 1.4 TB (fastq) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Hisashi Hasumi
Affiliation: Department of Urology, Yokohama City University
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Analysis on the mechanism of renal tumorigenesis focusing on the metabolic and membrane transport regulation of FLCN | 19K09694 |
| the MEXT Joint Usage/Research Center Program | The Advanced Medical Research Center of Yokohama City University "Center for Advanced Medical Research Collaboration in Multi-omics Gene Expression Regulation" |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Single-cell transcriptomes underscore genetically distinct tumor characteristics and microenvironment for hereditary kidney cancers | doi: 10.1016/j.isci.2022.104463 | JGAD000414 |
| 2 | Comparative analyses define differences between BHD-associated renal tumor and sporadic chromophobe renal cell carcinoma | doi: 10.1016/j.ebiom.2023.104596 | JGAD000686 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
| Antonio Finelli | University Health Network/Princess Margaret Cancer Center | Canada | Identifying novel immune evasion tumor immune networks as targets for ccRCC immunotherapy | JGAD000414, JGAD000686 | 2023/11/16-2025/08/31 |
