NBDC Research ID: hum0127.v2
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SUMMARY
Aims: clarify the molecular profiling and sequential somatic mutation shift in hypermutator tumors harborig POLE mutations
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 and Microarray.
Participants/Materials:
JGAS000130: 91 hypermutated solid tumors that obtained from patients who take surgeries to remove cancers at the Shizuoka Cancer Center Hospital
JGAS000274: Fresh frozen tumors and blood cells obtained from 5143 cancer patients who take surgeries to remove cancers at the Shizuoka Cancer Center Hospital
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 |
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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 (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 (NBDC-91sample.renamed.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 |
| Participants/Materials |
Tumor tissue of 5063 Japanese cancer patients Non cancerous tissue of 5063 Japanese cancer patients (ICD10: C00-D48) |
| 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 | JGAD000380 |
| Total Data Volume |
27.3 MB (HOPE-5000.GEP.tumor.tab) 27.4 MB (HOPE-5000.GEP.normal.tab) |
| Comments (Policies) | NBDC policy |
JGAS000274 (RNA Amplicon-seq)*ref5
| Participants/Materials |
Tumorr 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 |
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 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|
| Koshi Mimori | Department of Surgery, Kyushu University Beppu Hospital | Transomic analysis of molecular characterization of Japanese breast cancer | JGAD000141, JGAD000380 | 2021/05/24-2022/06/30 |
| Masaki Mandai | Kyoto University Faculty of Medicene, department of Gynecology and Obstetrics | Integrated analyses of omics (genomics, transcriptomics, proteomics and metabolomics) associated with clinical variables for developing indivisualizedtreatment in gynecological malignancy | JGAD000141, JGAD000380 | 2021/10/14-2025/03/31 |
