NBDC Research ID: hum0094.v1

SUMMARY

Aims: Identification of oncogenic alteration in breast cancer through genomic analysis.

Methods: Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), and RNA-seq were performed with HiSeq 2000/2500.

Participants/Materials: Surgically resected breast cancer tissues and paired non-tumor tissues or peripheral blood cells (as normal tissues)

WES: Triple negative breast cancer: 36 cases (including 16 cases used for WGS and 23 cases used for RNA-seq)

WGS: Triple negative breast cancer: 16 cases

RNA-seq: Triple negative breast cancer: 23 cases

Estrogen receptor-positive breast cancer: 17 cases

Human epidermal growth factor receptor 2 (HER2)-positive breast cancer: 15 cases

URL： https://www.ncc.go.jp/en/ri/division/genetics/index.html

Data Set ID	Type of Data	Criteria	Release Date
JGAS000095	NGS (WGS, Exome, RNA-seq)	Controlled Access (Type I)	2017/09/04

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MOLECULAR DATA


Participants/Materials	Triple negative breast cancer (ICD10: C50): 16 cases
Targets	WGS
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq 2000/2500]
Library Source	DNAs extracted from breast cancer tissues and paired non-tumor tissues or peripheral blood cells
Cell Lines	-
Library Construction (kit name)	NEBNext® Ultra™ DNA Library Prep Kit for Illumina®
Fragmentation Methods	Ultrasonic fragmentation (Covaris)
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	103 bp
Japanese Genotype-phenotype Archive Data set ID	JGAD000095
Total Data Volume	8 TB (bam [ref: hg19])
Comments (Policies)	NBDC policy


Participants/Materials	Triple negative breast cancer (ICD10: C50): 36 cases
Targets	Exome
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq 2000/2500]
Library Source	DNAs extracted from breast cancer tissues and paired non-tumor tissues or peripheral blood cells
Cell Lines	-
Library Construction (kit name)	NEBNext® Ultra™ DNA Library Prep Kit for Illumina®, SureSelect Human All Exon V5
Fragmentation Methods	Ultrasonic fragmentation (Covaris)
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	103 bp
Japanese Genotype-phenotype Archive Data set ID	JGAD000095
Total Data Volume	8 TB (bam [ref: hg19])
Comments (Policies)	NBDC policy


Participants/Materials	Triple negative breast cancer (ICD10: C50): 23 cases Estrogen receptor-positive breast cancer (ICD10: C50): 17 cases HER2-positive breast cancer (ICD10: C50): 15 cases
Targets	RNA-seq
Target Loci for Capture Methods	-
Platform	Illumina [HiSeq 2000/2500]
Library Source	RNAs extracted from breast cancer tissues
Cell Lines	-
Library Construction (kit name)	NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®
Fragmentation Methods	Heat treatment
Spot Type	Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers)	103 bp
Japanese Genotype-phenotype Archive Data set ID	JGAD000095
Total Data Volume	8 TB (fastq)
Comments (Policies)	NBDC policy

Principal Investigator: Hiroyuki Mano

Affiliation: Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo

Project / Group Name: -

URL： https://www.ncc.go.jp/en/ri/division/genetics/index.html

Funds / Grants (Research Project Number):

Name	Title	Project Number
The Japan Agency for Medical Research and Development (AMED)	Project for novel therapeutic targets in cancer	-
KAKENHI Grant-in-Aid for Scientific Research (C)	Oncogenic mutations of RAC small GTPases in Human cancers	26430106
Grant from The Princess Takamatsu Cancer Research Fund	Analysis of molecular mechanisms of oncogenic activity of RAC small GTPase	-

	Title	DOI	Data Set ID
1	Integrative analysis of genomic alterations in triple-negative breast cancer in association with homologous recombination deficiency	doi: 10.1371/journal.pgen.1006853	JGAD000095

Principal Investigator:	Affiliation:	Data in Use (Data Set ID)	Period of Data Use