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Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HumanRef-v3 samples]

ABSTRACT: We performed an expression profiling study of 168 primary breast tumors, lymph node metastases, and autopsy samples of primary breast tumours and metastases to liver, chest wall, lymph node, lung, and spleen, as well as positive and negative RNA controls, with technical replicates, to assess quality control methodology and probe-level reproducibility of the Illumina DASL microarray assay. The experiment included both Illumina DASL HumanRef-v3 and DASL HT-12; this series includes only the 120 HumanRef-v3 samples .

ORGANISM(S): Homo sapiens

PROVIDER: GSE32489 | GEO | 2012/10/02

SECONDARY ACCESSION(S): PRJNA154443

REPOSITORIES: GEO

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Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HumanRef-v3 samples]

Project description:We performed an expression profiling study of 168 primary breast tumors, lymph node metastases, and autopsy samples of primary breast tumours and metastases to liver, chest wall, lymph node, lung, and spleen, as well as positive and negative RNA controls, with technical replicates, to assess quality control methodology and probe-level reproducibility of the Illumina DASL microarray assay. The experiment included both Illumina DASL HumanRef-v3 and DASL HT-12; this series includes only the 120 HumanRef-v3 samples . This series includes 120 samples in total: 19 autopsy tissues of the chest wall, liver, lymph nodes, lung, spleen, liver, and breast, 5 negative controls, 6 positive controls, and 90 lymph node metastases.

2012-10-02 | E-GEOD-32489 | biostudies-arrayexpress

Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HT-12 samples]

2012-10-02 | GSE32488 | GEO

Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HT-12 samples]

Project description:We performed an expression profiling study of 168 primary breast tumors, lymph node metastases, and autopsy samples of primary breast tumours and metastases to liver, chest wall, lymph node, lung, and spleen, as well as positive and negative RNA controls, with technical replicates, to assess quality control methodology and probe-level reproducibility of the Illumina DASL microarray assay. The experiment included both Illumina DASL HumanRef-v3 and DASL HT-12; this series includes only the 48 HT12 samples . This series includes 48 samples in total: 9 positive controls, 4 negative controls, and 35 primary breast tumors and metastatic lymph nodes.

2012-10-02 | E-GEOD-32488 | biostudies-arrayexpress

Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues

Project description:This SuperSeries is composed of the following subset Series: GSE32488: Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HT-12 samples] GSE32489: Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HumanRef-v3 samples] Refer to individual Series

2012-10-02 | E-GEOD-32490 | biostudies-arrayexpress

Homo sapiens

Project description:Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HumanRef-v3 samples]

| PRJNA154443 | ENA

Breast cancer tumors

Project description:The project analyzed 88 breast cancer clinical samples, including lymph node negative and positive primary tumors, lymph node metastases, and healthy tissue as control. All samples were combined with a super-SILAC mix that served as an internal standard for quantification.

2016-06-16 | MSV000079830 | MassIVE

Breast cancer tumors - System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis

2016-01-25 | PXD000815 | Pride

WG-DASL expression profiling of formalin-fixed paraffin embedded primary breast tumours and matched lymph node metastases across four clinically relevant metastatic groups

Project description:The development of metastases is a complex multi-step process manifested by diverse patterns, involving single or multiple organs and different time-courses of distant recurrences. The aim of this study was to characterise molecular patterns associated with patterns of organ-specific metastatic spread observed in the clinic from FFPE embedded breast carcinomas and lymph node metastases. This study includes patients with four patterns of first metastatic sites: bone only (with no visceral metastases within 6 months of first metastasis); to viscera only (with no bone metastasis within 6 months of first metastasis); to bone and visceral organs within a 6 month period; and no recorded distant metastasis. The study population was composed of 5,061 patients diagnosed with invasive primary breast cancer without distant metastasis at the time of diagnosis between 1975 and 2005 from Guyâs Hospital. From the study population, an incidence-based case-control design was used to include patients from each of the metastatic groups and a control series randomly matched to cases according to having no reported metastasis up to the calendar date of metastasis. The aim of this expression profiling study was to characterise any molecular patterns that may be associated with the organ-specific metastatic spread observed in the clinic from FFPE embedded breast carcinomas and lymph node metastases.

2017-12-01 | E-MTAB-4003 | biostudies-arrayexpress

Transcriptomic survey of lymph node-positive vs. - negative ductal breast cancer

Project description:Lymph node involvement is a major prognostic variable in breast cancer. Whether the molecular mechanisms that drive breast cancer cells to colonize lymph nodes are shared with their capacity to form distant metastases is yet to be established. In a transcriptomic survey aimed at identifying molecular factors associated with lymph node involvement of ductal breast cancer, we found that luminal differentiation, assessed by the expression of estrogen receptor (ER) and/or progesterone receptor (PR) and GATA3, was only infrequently lost in node-positive primary tumors and in matched lymph node metastases. The transcription factor GATA3 critically determines luminal lineage specification of mammary epithelium and is widely considered a tumor and metastasis suppressor in breast cancer. Strong expression of GATA3 and ER in a majority of primary node-positive ductal breast cancer was corroborated by quantitative RT-PCR and immunohistochemistry in the initial sample set, and by immunohistochemistry in an additional set from 167 patients diagnosed of node-negative and positive primary infiltrating ductal breast cancer, including 102 samples from loco-regional lymph node metastases matched to their primary tumors, as well as 37 distant metastases. These observations suggest that loss of luminal differentiation is not a major factor driving the ability of breast cancer cells to colonize regional lymph nodes. The transcriptomic study comprises 16 samples from Lymph node metastasis from infiltrating ductal breast carcinoma, 18 samples from Primary node-positive infiltrating ductal,7 samples from Primary node-negative infiltrating ductal and 3 samples from Unaffected lymph node were included. Their RNA was isolated and prepared for hybridization to human Affymetrix GeneChip arrays.

2013-03-05 | E-GEOD-44408 | biostudies-arrayexpress

Desorption electrospray ionisation mass spectrometry imaging of esophageal lymph mode metastases

Project description:Lymph node metastases (LNM) and primary tumour samples were analysed using desorption electrospray ionisation mass spectrometry imaging (DESI MSI). Current assessment of LNM depends on subjective histopathological assessment, whereas analysis by DESI MSI permits an entirely objective assessment. The mass spectral data revealed specific lipidomic patterns across samples, which were shown to correspond to the immunohistochemical image. Statistical prediction of LNM samples was performed using the esophageal adenocarcinoma samples with sensitivity and specificity of 89.5% and 100%, respectively.

2017-01-10 | MTBLS385 | MetaboLights

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