NBDC Research ID: hum0200.v4
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SUMMARY
Aims: Search for risk stratification factors based on the molecular biological background of non-invasive ductal carcinoma
Methods: Select DCIS cases based on clinical risk factors. Examine association with risk factors by comprehensive gene analysis.
Participants/Materials: Human Ductal Carcinoma In Situ (DCIS), Invasive Ductal Carcinoma (IDC)
| Data Set 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 |
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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 Data set 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 Data set 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 Data set 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 Data set 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 Data set 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 Data set ID | |
| Total Data Volume |
JGAD000308：259 GB (fastq, tif) JGAD000396：594.7 GB (fastq, tif, tsv) |
| 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 | Data Set 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 | Research Title | Data in Use (Data Set ID) | Period of Data Use |
|---|---|---|---|---|
