NBDC Research ID: hum0094.v2

 

SUMMARY

Aims: Identification of oncogenic alteration in breast cancer and lung adenocarcinoma 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)

                       Lung adenocarcinoma : 43 cases

            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

                            Lung adenocarcinoma : 43 cases

URL: http://mano-lab.umin.jp/english/index.html

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000095 NGS (WGS, Exome, RNA-seq) Controlled Access (Type I) 2017/09/04
JGAS00000000105 NGS (Exome, RNA-seq) Controlled Access (Type I) 2018/01/22

*Release Note

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

WGS

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 tumor tissues and paired non-tumor tissues or peripheral blood cells as non-tumor tissues
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 JGAD00000000095
Total Data Volume 8 TB (bam [ref: hg19])
Comments (Policies) NBDC policy

 

Exome

Participants/Materials

Triple negative breast cancer (ICD10: C50): 36 cases

Lung adenocarcinoma (ICD10: C349): 43 cases

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000/2500]
Library Source DNAs extracted from tumor tissues and paired non-tumor tissues or peripheral blood cells as non-tumor tissues
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

Triple negative breast cancer: JGAD00000000095

Lung adenocarcinoma: JGAD00000000110 (bam)

Total Data Volume 10 TB (bam [ref: hg19/hg38])
Comments (Policies)

NBDC policy (JGAD00000000095)

NBDC policy & Company User Limit (JGAD00000000110)

 

RNA-seq

Participants/Materials

Triple negative breast cancer (ICD10: C50): 23 cases

Estrogen receptor-positive breast cancer (ICD10: C50): 17 cases

HER2-positive breast cance (ICD10: C50)r: 15 cases

Lung adenocarcinoma (ICD10: C349): 43 cases

Targets RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 2000/2500]
Library Source RNAs extracted from tumor 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

Breast cancers: JGAD00000000095

Lung adenocarcinoma: JGAD00000000111 (fastq)

Total Data Volume 10 TB (fastq)
Comments (Policies)

NBDC policy (JGAD00000000095)

NBDC policy & Company User Limit (JGAD00000000111)

 

DATA PROVIDER

Principal Investigator: Hiroyuki Mano

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

Project / Group Name: -

URL: http://mano-lab.umin.jp/english/index.html

Funds / Grants (Research Project Number):

NameTitleProject Number
Leading Advanced Projects for medical innovation, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-LEAP) 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 -

 

PUBLICATIONS

TitleDOIData 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 JGAD00000000095
2 Inactivating mutations and hypermethylation of the NKX2-1/TTF-1 gene in non-terminal respiratory unit-type lung adenocarcinomas. doi: 10.1111/cas.13313 JGAD00000000110, JGAD00000000111

 

USERS (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use
Subhajyoti De Rutgers Cancer Institute, Rutgers the State University of New Jersey JGAD00000000095 2018/08/06-2021/05/31
Youping Deng Department of Complementary and Integrative Medicine, University of Hawai Manoa JGAD00000000110, JGAD00000000111 2018/10/04-2025/07/10