NBDC Research ID: hum0200.v5

 

SUMMARY

Aims: Search for risk stratification factors based on the molecular biological background of non-invasive ductal carcinoma

Methods: Selected the patients with Ductal Carcinoma In Situ (DCIS) or Invasive Ductal Carcinoma (IDC) based on clinical risk factors and examined the association with risk factors by comprehensive gene analyses.

- IDC: target capture sequencing (TC), Methylation, Spatial Gene Expression, single-cell RNA sequencing (scRNA-seq), and semibulk RNA-seq analyses

- DCIS: In addition to the above analyses, whole exome sequencing (Exome), single-cell copy number variant (scCNV), and whole genome sequencing (WGS) analyses

Participants/Materials: Human Ductal Carcinoma In Situ (DCIS), Invasive Ductal Carcinoma (IDC)

 

Dataset IDType of DataCriteriaRelease Date
JGAS000202

NGS (Exome)

single-cell CNV analysis

Controlled-access (Type I) 2021/03/29
JGAS000265

NGS (WGS)

Methylation analysis

Controlled-access (Type I) 2021/05/07
JGAS000202 (Data addition)

NGS (Target Capture)

NGS (Visium Spatial Gene Expression), Histological image

Controlled-access (Type I) 2021/10/01
JGAS000290 NGS (Visium Spatial Gene Expression), Histological image Controlled-access (Type I) 2022/03/02
JGAS000387

NGS (semibulk RNA-seq)

NGS (scRNA-seq)

Controlled-access (Type I) 2022/8/29

*Release Note  

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

 

MOLECULAR DATA

Exome

Participants/Materials

DCIS (ICD10: D051): 24 cases

      tumor tissues: 28 samples

      non-tumor tissues: 24 samples

Targets Exome
Target Loci for Capture Methods -
Platform Illumina [HiSeq 3000]
Library Source DNAs extracted from tumor and non-tumor tissues
Cell Lines -
Library Construction (kit name) SureSelect Human All Exon V7
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 200 bp
Japanese Genotype-phenotype Archive Dataset ID JGAD000287
Total Data Volume 775 GB (fastq)
Comments (Policies) NBDC policy

 

single-cell CNV analysis

Participants/Materials

DCIS (ICD10: D051): 3 cases

      tumor tissues: 3 samples

Targets single-cell CNV
Target Loci for Capture Methods -
Platform 10x Genomics [Chromium Controller]
Source single-cells from tumor tissues
Cell Lines -
Library Construction (kit name) Chromium Single-Cell DNA Reagent Kit (10x Genomics)
Algorithm for detecting CNVs (software) cellranger-dna-1.1.0 (refdata-GRCh38-1.0.0.)
Filtering Methods cellranger-dna-1.1.0
CNV number -
Japanese Genotype-phenotype Archive Dataset ID JGAD000287
Total Data Volume 775 GB (fastq)
Comments (Policies) NBDC policy

 

WGS

Participants/Materials

DCIS (ICD10: D051): 2 cases

      tumor tissues: 2 samples

      non-tumor tissues: 2 samples

Targets WGS
Target Loci for Capture Methods -
Platform

Illumina [NovaSeq 6000]

Nanopore [PromethION]

Library Source DNAs extracted from tumor and non-tumor tissues
Cell Lines -
Library Construction (kit name)

Illumina: TruSeq DNA Nano

Nanopore: SQK_LSK109

Fragmentation Methods

Illumina: Ultrasonic fragmentation (Covaris M220)

Nanopore: -

Spot Type

Illumina: Paired-end

Nanopore: Single-end

Read Length (without Barcodes, Adaptors, Primers, and Linkers)

Illumina: 300 bp

Nanopore: -

Japanese Genotype-phenotype Archive Dataset ID JGAD000368
Total Data Volume 873 GB (fastq)
Comments (Policies) NBDC policy

 

Methylation analysis

Participants/Materials

DCIS (ICD10: D051): 1 cases

IDC (ICD10: C509): 2 cases

      tumor tissues: 4 samples

      non-tumor tissues: 3 samples

Targets Methylation analysis
Target Loci for Capture Methods -
Platform Nanopore [PromethION]
Source DNAs extracted from tumor and non-tumor tissues
Cell Lines -
Reagents (Kit, Version) SQK_LSK109
Algorithms for Calculating Methylation-rate (software) Nanopolish
Japanese Genotype-phenotype Archive Dataset ID JGAD000368
Total Data Volume 873 GB (fastq, tsv [ref: GRCh38.p12])
Comments (Policies) NBDC policy

 

Target Capture

Participants/Materials

IDC (ICD10: C509): 2 cases

DCIS (ICD10: D051): 72 cases

Targets Target Capture
Target Loci for Capture Methods 180 genes
Platform Illumina [NovaSeq 6000]
Library Source DNAs extracted from tumor tissues
Cell Lines -
Library Construction (kit name) SureSelect XT custom capture library
Fragmentation Methods Ultrasonic fragmentation (Covaris)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 200 bp (100 PE)
Japanese Genotype-phenotype Archive Dataset ID JGAD000307
Total Data Volume 455 GB (fastq)
Comments (Policies) NBDC policy

 

Visium Spatial Gene Expression, Histological image (JGAS000202, JGAS000290)

Participants/Materials

IDC (ICD10: C509): 2 cases

DCIS (ICD10: D051): 1 case

Targets Visium Spatial Gene Expression, Histological image
Target Loci for Capture Methods -
Platform Illumina [NovaSeq 6000]
Library Source RNAs extracted from tumor tissues
Cell Lines -
Library Construction (kit name) Visium Spatial Gene Expression Reagent Kits
Fragmentation Methods -
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 148 bp (28/120 PE)
Japanese Genotype-phenotype Archive Dataset ID

JGAD000308

JGAD000396

Total Data Volume

JGAD000308:259 GB (fastq, tif)

JGAD000396:594.7 GB (fastq, tif, tsv)

Comments (Policies) NBDC policy

 

semibulk RNA-seq

Participants/Materials

DCIS (ICD10: D051): 1 case

      tumor tissues: 2 libraries from 1 sample

IDC (ICD10: C509): 1 case

      tumor tissues: 2 libraries from 1 sample

Targets semibulk RNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 3000, NovaSeq 6000]
Source Semibulks (cell clumps) prepared from tumor tissues
Cell Lines -
Library Construction (kit name) Drop-Seq Laboratory Protocol, version 3.1
Fragmentation Methods Tagmentation with Nextera XT (Illumina)
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 200 bp (100PE)
Japanese Genotype-phenotype Archive Dataset ID JGAD000502
Total Data Volume 272.4 GB (fastq)
Comments (Policies) NBDC policy

 

scRNA-seq

Participants/Materials

DCIS (ICD10: D051): 1 case

      tumor tissues: 1 sample

      non-tumor tissues: 1 sample

IDC (ICD10: C509): 1 case

      tumor tissues: 1 sample

      non-tumor tissues: 1 sample

Targets scRNA-seq
Target Loci for Capture Methods -
Platform Illumina [HiSeq 3000]
Source Single cells obtained from tumor and non-tumor tissues
Cell Lines -
Library Construction (kit name) Chromium single cell 3’ kit version 3 (10x Genomics)
Fragmentation Methods enzymatic fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 124 bp (26/98PE)
Japanese Genotype-phenotype Archive Dataset ID JGAD000502
Total Data Volume 272.4 GB (fastq)
Comments (Policies) NBDC policy

*This study was supported by "Genome Science". "Genome Science" is a part of the "Support Programs for Three Fields in Life Sciences (cancer, genome, and brain sciences)" established by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) under the Grant-in-Aid for Scientific Research on Innovative Areas.

 

DATA PROVIDER

Principal Investigator: Satoi Nagasawa

Affiliation: Division of Breast and Endocrine Surgery, Department of Surgery St. Marianna University School of Medicine

Project / Group Name: -

Funds / Grants (Research Project Number):

NameTitleProject Number
JSPS Fujita Memorial Fund for Medical Research Investigation of novel risk factors for recurrence to optimize the treatment of ductal carcinoma in situ (DCIS) of the breast -
KAKENHI Grant-in-Aid for Scientific Research on Priority Areas (Research in a proposed research area) Platform for Advanced Genome Science 16H06279 (PAGS)

 

PUBLICATIONS

TitleDOIDataset ID
1 Efficient prediction of a spatial transcriptomics profile better characterizes breast cancer tissue sections without costly experimentation doi: 10.1038/s41598-022-07685-4 JGAD000396
2

 

USRES (Controlled-access Data)

Principal InvestigatorAffiliationCountry/RegionResearch TitleData in Use (Dataset ID)Period of Data Use