NBDC Research ID: hum0127.v3
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
URL: https://www.scchr.jp/en/institute/projecthope.html
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000130 | NGS (Exome) | Controlled-access (Type I) | 2020/04/14 |
| JGAS000274 | Controlled-access (Type I) | 2021/03/08 | |
| JGAS000604 | Controlled-access (Type I) | 2024/01/22 |
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MOLECULAR DATA
| 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 |
| 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 |
| 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 |
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
| Title | DOI | Dataset 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 Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
