NBDC Research ID: hum0127.v2

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

Data Set ID	Type of Data	Criteria	Release 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

Data Set ID

Type of Data

Criteria

Release 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

*Release Note

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

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 (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 Data set 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 Data set 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 Data set 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 Data set 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 Data set ID	JGAD000380
Total Data Volume	2.19 MB (HOPE-5000.CCP.somatic-mutation.vcf [ref: hg19])
Comments (Policies)	NBDC policy

JGAS000274 (Microarray)^*ref4


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 Data set 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 Data set 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	Data Set 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 (Data Set 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