Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sequence of Primary ER+ Breast Tumors Treated with 5 Years of Tamoxifen

ABSTRACT:

Targeted massively parallel sequencing analysis was conducted on DNA extracted from archived 22-28 year old, formalin-fixed primary breast tumors from 625 patents from British Columbia treated with five years of adjuvant tamoxifen monotherapy and followed for over 10 years. Genes were selected for targeted sequencing by review of existing large-scale breast cancer sequencing studies and breast cancer literature. In total, 83 genes were identified and 3,029 probes were designed to tile across all known exons. Illumina sequencing libraries were constructed, indexed, pooled, and enriched for target sequences by hybrid-capture followed by sequencing of paired-end 100bp reads. All samples met minimum quality controls of 80% targeted space covered at 20X or greater. On average, each sample had 336M aligned bases and a mean coverage of 135.8X.

PROVIDER: phs001234 | dbGaP |

SECONDARY ACCESSION(S): PRJNA350582PRJNA350581

REPOSITORIES: dbGaP

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	GapExchange_phs001234.v1.p1.xml	Xml
	dbGaPEx2.1.5.xsd	Other
	Study_Report.phs001234.ERpositiveBreastTumors_Tamoxifen.v1.p1.MULTI.pdf	Pdf
	manifest_phs001234.ERpositiveBreastTumors_Tamoxifen.v1.p1.c1.DS-CA-IRB.pdf	Pdf
	datadict_v2.xsl	Other

Items per page:

1 - 5 of 13

Similar Datasets

Phase I study of Veliparib in combination with Cisplatin and Vinorelbine for patients with advanced triple-negative breast cancer (TNBC) and/or BRCA mutation-associated breast cancer

Project description:PURPOSE: Preclinically, cisplatin is synergistic with vinorelbine and the poly(ADP-ribose) polymerase (PARP) inhibitor veliparib, and has anti-neoplastic activity in TNBC and BRCA mutation-associated breast cancer. This phase I study assessed veliparib with cisplatin and vinorelbine. PATIENTS AND METHODS: A 3+3 dose escalation design evaluated veliparib administered BID for 14 days with cisplatin (75 mg/m2 day 1) and vinorelbine (25 mg/m2 days 1,8) every 21 days, for six to ten cycles, followed by veliparib monotherapy. Pharmacokinetics, measurement of poly(ADP-ribose) in peripheral blood mononuclear cells, and preliminary efficacy were assessed. Immunohistochemistry and gene expression profiling were performed to evaluate potential predictors of response. Thirty-nine samples were assessed, six samples were run as technical duplicates. Two of the samples had a high rate of missing probes and were excluded during the normalization/pre-processing. Each sample represents a pre- or post-treatment breast cancer specimen from individual patients.

2015-09-09 | E-GEOD-72795 | biostudies-arrayexpress

caArray_gray-00215: A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes

Project description:Recent studies suggest that thousands of genes may contribute to breast cancer pathophysiologies when deregulated by genomic or epigenomic events. Here, we describe a model system to appraise the functional contributions of these genes to breast cancer subsets. In general, the recurrent genomic and transcriptional characteristics of 51 breast cancer cell lines mirror those of 145 primary breast tumors, although some significant differences are documented. The cell lines that comprise the system also exhibit the substantial genomic, transcriptional, and biological heterogeneity found in primary tumors. We show, using Trastuzumab (Herceptin) monotherapy as an example, that the system can be used to identify molecular features that predict or indicate response to targeted therapies or other physiological perturbations. **NOTE: Migrated from caArray 1.x, identifier='gov.nih.nci.ncicb.caarray:Experiment:1015897590151581:1' gray-00215 Assay Type: Gene Expression Provider: Affymetrix Array Designs: HG-U133A Organism: Homo sapiens (ncbitax)

2015-05-19 | E-GEOD-69017 | biostudies-arrayexpress

Next generation sequencing for patients with hypomyelinating leukodystrophies

Project description:Targeted enrichment-based next-generation sequencing or whole exome sequencing were taken for patients with hypomyelinating leukodystrophies to reveal genetic aetiologies. All genomic DNA used in the experiments was extracted from the peripheral leukocytes. A complete kit was synthetized using the Agilent SureSelect Target Enrichment technique, capturing the coding regions from 104 candidate genes, including their exons and exon-intron boundaries (11,473 probes, 383.065 kbp in total). The following NGS which included equipment and reagents was performed on an Illumina NEXTSEQ500 platform manufactured by Illumina (San Diego, California, USA) using paired-end sequencing of 110 bp. The clean paired-end reads were aligned to the human reference genome build hg19, which was previously annotated using ANNOVAR, in addition to insertion-deletion (indel) and single-nucleotide polymorphism (SNP) calling.

2018-02-01 | E-MTAB-6054 | biostudies-arrayexpress

Next generation sequencing for patients with hypomyelinating leukodystrophies

2018-02-02 | E-MTAB-6404 | biostudies-arrayexpress

Homo sapiens

Project description:breast cancer / tamoxifen monotherapy (microdissected tumor biopsies)

| PRJNA90027 | ENA

breast cancer / tamoxifen monotherapy (whole tissue tumor biopsies)

Project description:dataset of 60 patients with ER-positive primary breast cancer and treated with tamoxifen monotherapy for 5 years. Data were generated from whole tissue sections of breast cancers. Sample_keyword: breast cancer, tamoxifen, recurrence Keywords: other

2004-06-07 | GSE1379 | GEO

caArray_gray-00215: A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes

2015-05-19 | GSE69017 | GEO

Homo sapiens

Project description:breast cancer / tamoxifen monotherapy (whole tissue tumor biopsies)

| PRJNA90165 | ENA

Targeted partial reprogramming of age-associated cell states improves markers of health in mouse models of aging

Project description:The study aims to explore the effects of CDKN2A-OSK expression across various tissues and human primary cells using next-generation sequencing. Mouse tissues and human cultured cells were collected at specific time points, followed by RNA extraction and next-generation sequencing. The sequencing data for mouse RNA were aligned to the mm9 genome, while the human RNA data were aligned to the Hg38 genome using standard RNA alignment and analysis protocols.

2024-11-12 | GSE201710 | GEO

breast cancer / tamoxifen monotherapy (microdissected tumor biopsies)

Project description:dataset of 60 patients with ER-positive primary breast cancer and treated with tamoxifen monotherapy for 5 years. Data were generated from LCMed cancer cells. Sample_keyword: breast cancer, tamoxifen, recurrence Keywords: other

2004-06-07 | GSE1378 | GEO