NBDC Research ID: hum0200.v6
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), semibulk RNA-seq, whole genome sequencing (WGS), Enzymatic Methyl-seq (EM-seq), targeted long-read methylation sequencing (t-nanoEM) analyses
- DCIS: target capture sequencing (TC), methylation, spatial gene expression, single-cell RNA sequencing (scRNA-seq), semibulk RNA-seq, 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 ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000202 | Controlled-access (Type I) | 2021/03/29 | |
| JGAS000265 | Controlled-access (Type I) | 2021/05/07 | |
| JGAS000202 (Data addition) | Controlled-access (Type I) | 2021/10/01 | |
| JGAS000290 | NGS (Visium Spatial Gene Expression), Histological image | Controlled-access (Type I) | 2022/03/02 |
| JGAS000387 | Controlled-access (Type I) | 2022/08/29 | |
| JGAS000758 | NGS (WGS, RNA-seq, EM-seq, t-nanoEM) | Controlled-access (Type I) | 2024/11/25 |
*Data users need to apply an application for Using NBDC Human Data to reach the Controlled-access Data. Learn more
MOLECULAR DATA
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | |
| Total Data Volume |
JGAD000308：259 GB (fastq, tif) JGAD000396：594.7 GB (fastq, tif, tsv) |
| Comments (Policies) | NBDC policy |
| 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 |
| 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 |
| Participants/Materials |
IDC (ICD10: C509): 1 case 4 microdissected tissues from breast cancer sections (tumor tissues: 2 samples*, non-tumor tissues: 2 samples*) |
| Targets | WGS |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Enzymatic Methyl-seq Kit without procedures for base conversion. |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000899 |
| Total Data Volume | 774.0 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
IDC (ICD10: C509): 1 case 4 microdissected tissues from breast cancer sections (tumor tissues: 2 samples, non-tumor tissues: 2 samples) |
| Targets | RNA-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Source | RNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | SMART-seq Stranded Kit |
| Fragmentation Methods | Heat treatment with Shearing Master Mix |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000899 |
| Total Data Volume | 774.0 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
IDC (ICD10: C509): 1 case 4 microdissected tissues from breast cancer sections (tumor tissues: 2 samples*, non-tumor tissues: 2 samples*) |
| Targets | EM-seq |
| Target Loci for Capture Methods | - |
| Platform | Illumina [NovaSeq 6000] |
| Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | NEBNext Enzymatic Methyl-seq Kit |
| Fragmentation Methods | Ultrasonic fragmentation (Covaris) |
| Spot Type | Paired-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000899 |
| Total Data Volume | 774.0 GB (fastq) |
| Comments (Policies) | NBDC policy |
| Participants/Materials |
IDC (ICD10: C509): 1 case 4 microdissected tissues from breast cancer sections (tumor tissues: 2 samples*, non-tumor tissues: 2 samples*) |
| Targets | t-nanoEM |
| Target Loci for Capture Methods | Custom human methylome panel for long-read (Twist Bioscience, Order ID: MTE-9910638) |
| Platform | Nanopore [PromethION] |
| Source | DNAs extracted from tumor and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) |
NEBNext Enzymatic Methyl-seq Kit The five libraries were pooled and subjected to target enrichment using the Twist Standard Hyb and Wash Kit v2 with a pan-cancer panel. |
| Fragmentation Methods | g-TUBE (Covaris) |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 4,400 bp on average |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000899 |
| Total Data Volume | 774.0 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):
| Name | Title | Project 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
| Title | DOI | Dataset 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 Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
