NBDC Research ID: hum0273.v1
SUMMARY
Aims: Breast cancer manifests in diverse forms, with particular reference to various cell types harboring different mutations and gene expression profiles. To elucidate the clonal relationship between cancer cells in tumors composed of both ductal and lobular phenotypes, we analyzed two combined lobular and ductal carcinoma cases by next generation sequencing.
Methods: DNA from samples were used for amplicon sequencing by an Ion AmpliSeq Comprehensive Cancer Panel on an Ion Torrent platform (Thermo Fisher SCIENTIFIC). The panel consists of approximately 16,000 primer pairs covering all exons of 409 cancer-associated genes (1.6 megabases of target sequences). DNA (120 ng) was used to prepare the libraries with IonXpress barcoded adapters. An Ion Proton Sequencer (Thermo Fisher SCIENTIFIC) was used for sequencing with the ion chip.
Participants/Materials: A total of 9 DNAs collected by laser microdissection from 2 cases of lobular carcinoma in situ with ductal carcinoma in situ.
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000300 | NGS (Amplicon-seq) | Controlled-access (Type I) | 2021/08/27 |
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MOLECULAR DATA
| Participants/Materials |
lobular carcinoma in situ with ductal carcinoma in situ (ICD10: C509): 2 cases tumor tissues: 6 samples, non-tumor tissues: 3 samples |
| Targets | Amplicon-seq |
| Target Loci for Capture Methods | 409 genes (Ion Ampliseq Comprehensive Cancer Panel) |
| Platform | Thermo Fisher Scientific [Ion Proton] |
| Library Source | DNAs extracted from tumor tissues and non-tumor tissues |
| Cell Lines | - |
| Library Construction (kit name) | Ion Xpress Barcode Adapters |
| Fragmentation Methods | PCR amplification |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 100-300 bp |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000411 |
| Total Data Volume | 7.1 GB（bam） |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Shinobu Masuda
Affiliation: Division of Oncologic Pathology, Department of Pathology and Microbiology, Nihon University School of Medicine
Project / Group Name: -
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | A cell lineage of breast cancer consisting of different histologic types by mutation analysis of mtDNA D-loop region | 15K08357 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Phylogenetic analysis of combined lobular and ductal carcinoma of the breast | doi: 10.3892/mmr.2021.12357 | JGAD000411 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
