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 IDType of DataCriteriaRelease 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

*Release Note  

* Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more

 

MOLECULAR DATA

scRNA-seq

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

 

Exome

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

 

WGS

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):

NameTitleProject 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

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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