NBDC Research ID: hum0127.v4

 

SUMMARY

Aims: Blood and surgically removed tissues donated by approximately 1,000 cancer patients annually from Shizuoka Cancer Center's surgical cases are analyzed using multi-omics analysis technologies including genome, transcriptome, proteome, metabolome, and methylome. Tumor tissue analyses identified cancer driver genes and inherited cancer-causing genes in individual cancer patients and clarified the molecular profiling and sequential somatic mutation shift in hypermutator tumors harborig POLE mutations. Germline genome analysis will also be used to examine the presence or absence of hereditary cancers. Genetic polymorphisms of drug-metabolizing enzymes will be examined for associations with drug sensitivity and side effects. These results will be used to develop new drug discovery, diagnostics, and other treatment technologies.

Methods: DNAs and RNAs extracted from peripheral blood cells, tumor and non-tumor tissues are analyzed by whole-exome sequencing, DNA amplicon sequencing, RNA amplicon sequencing, microarray, Whole genome sequencing, and Methylation array.

Participants/Materials:

JGAS000130: 91 hypermutated solid tumors obtained from patients who had surgeries to remove cancers at the Shizuoka Cancer Center Hospital

JGAS000274: Fresh frozen tumors and blood cells obtained from 5143 cancer patients who had surgeries to remove cancers at the Shizuoka Cancer Center Hospital

JGAS000604: Gastrointestinal stromal tumor (GIST) 30 cases

JGAS000715: 177 cases in which no changes in driver genes were detected by whole exon sequencing and whole gene expression analysis in 5143 cancer patients who underwent surgery at Shizuoka Cancer Centre Hospital.

URL: https://www.scchr.jp/en/institute/projecthope.html

 

Dataset IDType of DataCriteriaRelease Date
JGAS000130 NGS (Exome) Controlled-access (Type I) 2020/04/14
JGAS000274

NGS (Exome; somatic mutation)

NGS (Exome; germline mutation)

NGS (Exome; CNV)

NGS (DNA Amplicon-seq, Exome)

Microarray

NGS (RNA Amplicon-seq)

Controlled-access (Type I) 2021/03/08
JGAS000604

NGS (WGS)

Microarray (Gene expression profiling)

Methylation array

Controlled-access (Type I) 2024/01/22
JGAS000715 NGS (WGS) Controlled-access (Type I) 2024/07/10

*Release Note

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

 

MOLECULAR DATA

JGAS000130 (Exome)

Participants/Materials

91 cancer patients with hypermutator tumors harborig POLE mutations

(ICD10: C00-D48)

Targets Exome
Target Loci for Capture Methods -
Platform Thermo Fisher Scientific [Ion Proton]
Library Source DNAs extracted from peripheral blood cells (non-tumor tissues) and surgically dissected tumor tissues
Cell Lines -
Library Construction (kit name) Ion AmpliSeq Exome RDY Kit
Fragmentation Methods -
Spot Type Single-end, multiplex PCR
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 180 bp
Mapping Methods Torrent Suite
QC methods Torrent Suite
Mutation Detection Methods Torrent Suite plugin Variant Caller
Japanese Genotype-phenotype Archive Dataset ID JGAD000141
Total Data Volume 75 MB (vcf [ref: hg19])
Comments (Policies) NBDC policy

 

JGAS000274 (Exome; somatic mutation)

Participants/Materials

Pair samples of tumor tissue and peripheral blood (white blood cell) from 5419 Japanese cancer patients

(ICD10: C00-D48)

Targets Exome
Target Loci for Capture Methods -
Platform Thermo Fisher Scientific [Ion Proton]
Library Source DNAs extracted from white blood cells (as a germ line) and surgically dissected tumor tissues
Cell Lines -
Library Construction (kit name) Ion AmpliSeq Exome RDY Kit
Fragmentation Methods -
Spot Type Single-end, multiplex PCR
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 180 bp
Mapping Methods Torrent Suite
QC methods Torrent Suite
Mutation Detection Methods Torrent Suite plugin Variant Caller
Japanese Genotype-phenotype Archive Dataset ID JGAD000380
Total Data Volume 36.5 MB (HOPE-5000.WES.somatic-mutation.vcf [ref: hg19])
Comments (Policies) NBDC policy

 

JGAS000274 (Exome; germline mutation)

Participants/Materials

White blood cells (as a germ line) of 5419 Japanese cancer patients

(ICD10: C00-D48)

Targets Exome
Target Loci for Capture Methods Hereditary tumor-associated genes (49 genes)
Platform Thermo Fisher Scientific [Ion Proton]
Library Source DNAs extracted from white blood cells
Cell Lines -
Library Construction (kit name) Ion AmpliSeq Exome RDY Kit
Fragmentation Methods -
Spot Type Single-end, multiplex PCR
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 180 bp
Mapping Methods Torrent Suite
QC methods Torrent Suite
Mutation Detection Methods Torrent Suite plugin Variant Caller
Japanese Genotype-phenotype Archive Dataset ID JGAD000380
Total Data Volume 12 KB (HOPE-5000.WES.germline-mutation.vcf [ref: hg19])
Comments (Policies) NBDC policy

 

JGAS000274 (Exome; CNV)

Participants/Materials

Pair samples of tumor tissue and peripheral blood (white blood cell) from 5433 Japanese cancer patients

Pair samples of tumor tissue and peripheral blood (white blood cell) from 5433 Japanese cancer patients

(ICD10: C00-D48)

Targets Exome
Target Loci for Capture Methods 880 genes (cancer driver gene and tumor supprresor gene)
Platform Thermo Fisher Scientific [Ion Proton]
Library Source DNAs extracted from peripheral blood cells (non-tumor tissues) and surgically dissected tumor tissues
Cell Lines -
Library Construction (kit name) Ion AmpliSeq Exome RDY Kit
Fragmentation Methods -
Spot Type Single-end, multiplex PCR
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 180 bp
Mapping Methods Torrent Suite
QC methods Torrent Suite
Mutation Detection Methods -
Japanese Genotype-phenotype Archive Dataset ID JGAD000380
Total Data Volume

6.77 MB (HOPE-5000.CNV.loss.tab)

6.26 MB (HOPE-5000.CNV.gain.tab)

Comments (Policies) NBDC policy

 

JGAS000274 (DNA Amplicon-seq, Exome)*ref3

Participants/Materials

Pair samples of tumor tissue and peripheral blood (white blood cell) from 5407 Japanese cancer patients

(ICD10: C00-D48)

Targets

DNA Amplicon-seq (tumor tissue)

Exome (white blood)

Target Loci for Capture Methods

a panel of 409 cancer related genes

Ion AmpliSeq Comprehensive Cancer Panel

Exome

Platform Thermo Fisher Scientific [Ion Proton]
Library Source DNAs extracted from white blood cells (as a germ line) and surgically dissected tumor tissues
Cell Lines -
Library Construction (kit name) Ion AmpliSeq™ Library Kit
Fragmentation Methods -
Spot Type Single-end, multiplex PCR
Read Length (without Barcodes, Adaptors, Primers, and Linkers)

100 bp (Panel)

180 bp (Exome)

Mapping Methods Torrent Suite
QC methods Torrent Suite
Mutation Detection Methods Torrent Suite plugin Variant Caller
Japanese Genotype-phenotype Archive Dataset ID JGAD000380
Total Data Volume 2.19 MB (HOPE-5000.CCP.somatic-mutation.vcf [ref: hg19])
Comments (Policies) NBDC policy

 

JGAS000274/JGAS000604 (Microarray)*ref4

Participants/Materials

Tumor tissue of 5063 Japanese cancer patients

Non cancerous tissue of 5063 Japanese cancer patients

(ICD10: C00-D48)

Gastrointestinal stromal tumor (GIST) (ICD10: C169): 30 cases

      tumor tissue: 30 samples

      paired peripheral blood cells: 29 samples

Targets Microarray
Target Loci for Capture Methods -
Platform

Chip: Agilent Technologies [SurePrint G3 Human Gene Expression 8 × 60 K v2 Microarray]

Scanner: Agilent Technologies [DNA Microarray Scanner]

Source RNA extracted from tumor and non-cancerous tissues
Cell Lines -
Reagents (Kit, Version) Low Input Quick Amp Labeling Kit One color
Filtering Methods The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Normalization of microarray 75 percentile
QC methods Agilent Feature Extraction software
Japanese Genotype-phenotype Archive Dataset ID

5063 Japanese cancer patients: JGAD000380

GIST: JGAD000733

Total Data Volume

Tumor tissue of 5063 Japanese cancer patients: 27.3 MB (HOPE-5000.GEP.tumor.tab)

Non cancerous tissue of 5063 Japanese cancer patients: 27.4 MB (HOPE-5000.GEP.normal.tab)

GIST: 1.3 GB (raw data about all probes: txt)

Comments (Policies) NBDC policy

 

JGAS000274 (RNA Amplicon-seq)*ref5

Participants/Materials

Tumor tissues of 95 Japanese cancer patients

(ICD10: C00-D48)

Targets RNA Amplicon-seq
Target Loci for Capture Methods Custom panel of 491 fusion genes
Platform Thermo Fisher Scientific [Ion Proton]
Library Source RNAs extracted from surgically dissected tumor tissues
Cell Lines -
Library Construction (kit name) Custom Panel / Ion AmpliSeq™ Library Kit
Fragmentation Methods -
Spot Type Single-end, multiplex PCR
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 100 bp
Mapping Methods Torrent Suite
QC methods Torrent Suite
Mutation Detection Methods Ion Reporter
Japanese Genotype-phenotype Archive Dataset ID JGAD000380
Total Data Volume 8 KB (HOPE-5000.Fusion.tab)
Comments (Policies) NBDC policy

 

JGAS000604 (WGS)

Participants/Materials

Gastrointestinal stromal tumor (GIST) (ICD10: C169): 30 cases

      tumor tissue: 30 samples

      paired peripheral blood cells: 30 samples

Targets WGS
Target Loci for Capture Methods -
Platform Illumina [NovaSeq 6000]
Library Source DNAs extracted from peripheral blood cells (non-tumor tissues) and surgically dissected tumor tissues
Cell Lines -
Library Construction (kit name) TruSeq DNA PCR-Free High Throughput Library Prep Kit
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Mapping Methods DRAGEN DNA Pipeline
Mapping Quality DRAGEN DNA Pipeline
Reference Genome Sequence hs37d5
Coverage (Depth)

Tumor samples: 130.3x (range: 115.7-150.7x)

Matched blood samples: 36.2x (range: 28.8-45.9x)

Detecting Methods for Variation Illumina DRAGEN Secondary Analysis
Japanese Genotype-phenotype Archive Dataset ID JGAD000733
Total Data Volume 1.3 GB (vcf)
Comments (Policies) NBDC policy

 

JGAS000604 (Methylation array)

Participants/Materials

Gastrointestinal stromal tumor (GIST) (ICD10: C169): 19 cases

      tumor tissue: 19 samples

      paired peripheral blood cells: 19 samples

Targets Methylation array
Target Loci for Capture Methods -
Platform Illumina [Infinium MethylationEPIC array, iScan System]
Library Source DNAs extracted from peripheral blood cells (non-tumor tissues) and surgically dissected tumor tissues
Cell Lines -
Library Construction (kit name) EZ DNA Methylation Kit, Infinium MethylationEPIC BeadChip
Algorithms for Calculating Methylation-rate (software) GenomeStudio Methylation Module v1.8
Filtering Methods -
Normalization of microarray -
Probe Number 866,836 probes
Japanese Genotype-phenotype Archive Dataset ID JGAD000733
Total Data Volume 1.3 GB (idat)
Comments (Policies) NBDC policy

 

JGAS000715 (WGS)

Participants/Materials

cancer (ICD10: C169, C170, C18 (180, 182, 184, 186, 187), C20, C220, C349, C433, C437, C445, C541, C56, C787, C793, C795, C08.1): 177 cases in which no changes in driver genes were detected by whole exon sequencing and whole gene expression analysis

      tumor tissue: 177 samples

      paired peripheral blood cells: 177 samples

Targets WGS
Target Loci for Capture Methods -
Platform Illumina [NovaSeq 6000]
Library Source DNAs extracted from peripheral blood cells (non-tumor tissues) and surgically dissected tumor tissues
Cell Lines -
Library Construction (kit name) TruSeq DNA PCR-Free High Throughput Library Prep Kit
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 150 bp
Mapping Methods DRAGEN DNA Pipeline
Mapping Quality DRAGEN DNA Pipeline
Reference Genome Sequence hs37d5
Coverage (Depth)

Tumor samples: 130.3x (range: 115.7-150.7x)

Matched blood samples: 36.2x (range: 28.8-45.9x)

Detecting Methods for Variation Illumina DRAGEN Secondary Analysis
Japanese Genotype-phenotype Archive Dataset ID JGAD000848
Total Data Volume 129.1 MB (tab, vcf)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Ken Yamaguchi

Affiliation: Shizuoka Cancer Center

Project / Group Name: Project HOPE (High-tech Omics-based Patient Evaluation) / Shizuoka Cancer Center

URL: https://www.scchr.jp/en/institute/projecthope.html

Funds / Grants (Research Project Number):

Name Title Project Number

 

PUBLICATIONS

TitleDOIDataset ID
1 Implementation of individualized medicine for cancer patients by multiomics-based analyses—the Project HOPE— doi: 10.2220/biomedres.35.407
2 Molecular profiling and sequential somatic mutation shift in hypermutator tumours harbouring POLE mutations doi: 10.1038/s41598-018-26967-4 JGAD000141
3 Integrated next-generation sequencing analysis of whole exome and 409 cancer-related genes doi: 10.2220/biomedres.37.367
4 Integrated analysis of gene expression and copy number identified potential cancer driver genes with amplification-dependent overexpression in 1,454 solid tumors doi: 10.1038/s41598-017-00219-3
5 Next generation sequencing approach for detecting 491 fusion genes from human cancer doi: 10.2220/biomedres.37.51
6 Japanese version of The Cancer Genome Atlas, JCGA, established using fresh frozen tumors obtained from 5143 cancer patients doi: 10.1111/cas.14290 JGAD000380
7 Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations 10.1158/2767-9764.CRC-22-0364 JGAD000733

 

USERS (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use
Noriomi Matsumura Department of Obstetrics and Gynecology, Faculty of Medicine, Kindai University Japan Integrated multi-omics analysis for ovarian clear cell adenocarcinoma: JGOG3017-TR1 JGAD000848 2024/10/15-2025/12/31
Ken Yamaguchi Gynecology and Obstetrics, Graduate School of Medicine and Faculty of Medicine, Kyoto University Japan Integrated multi-omics analysis for ovarian clear cell adenocarcinoma: JGOG3017-TR1 JGAD000848 2024/10/22-2025/12/31