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 IDType of DataCriteriaRelease Date
JGAS000300 NGS (Amplicon-seq) Controlled-access (Type I) 2021/08/27

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MOLECULAR DATA

JGAS000300

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):

NameTitleProject 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

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