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 IDType of DataCriteriaRelease Date
JGAS000544

NGS (WGS, Exome, RNA-seq)

Digital multiplexed gene expression analysis

Controlled-access (Type I) 2023/06/19

*Release Note

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

 

MOLECULAR DATA

WGS

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

 

Exome

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

 

RNA-seq

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):

NameTitleProject 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

TitleDOIDataset 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 InvestigatorAffiliationCountry/RegionResearch TitleData 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