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| Status |
Public on Mar 29, 2016 |
| Title |
Heterogeneity in global gene expression profiles between biopsy specimens taken peri-surgically from primary ER-positive breast carcinomas (excision/x-ray samples) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
Gene expression is widely used for the characterization of breast cancers. Variability due to tissue heterogeneity or measurement error or systematic change due to peri-surgical procedures can affect measurements but is poorly documented. We studied the variability of global gene expression between core-cuts of primary ER+ breast cancers and the impact of delays to tissue stabilization due to sample x-ray and of diagnostic core-cutting. Twenty-three and 56 sample pairs, respectively, were suitable for analysis. In general, there is a good correlation in gene expression between pairs of core-cuts except where genes have a narrow dynamic range. Increases in the expression of several stress/early-response genes (e.g., FOS, FOSB, JUN) were found in both studies. Substantial changes in expression of early response genes occur within an hour after surgery and in IL6, IGFB2 and MYC as a result of diagnostic core-cut biopsy. Similar correlation coefficients to the average gene expression profiles of intrinsic subtype, particularly LumA and LumB, can lead to discordances between assigned subtypes.
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| Overall design |
Twenty-three paired core-cuts were taken immediately after tumour excision and up to 60 minutes delay due to sample x-ray. Whole genome expression analysis was conducted on extracted RNA. Correlations and differences were assessed between the expression of individual genes, gene-sets/signatures and intrinsic subtypes.
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| Contributor(s) |
Gao Q |
| Citation(s) |
27036195 |
| Submission date |
Sep 20, 2015 |
| Last update date |
Feb 18, 2019 |
| Contact name |
Alice Gao |
| E-mail(s) |
alice.gao@icr.ac.uk
|
| Organization name |
The Institute of Cancer Research
|
| Department |
Breast Cancer Now
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| Lab |
Molecular Cell Biology
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| Street address |
237 Fulham Road
|
| City |
London |
| State/province |
London |
| ZIP/Postal code |
SW3 6JB |
| Country |
United Kingdom |
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| Platforms (2) |
| GPL6884 |
Illumina HumanWG-6 v3.0 expression beadchip |
| GPL10558 |
Illumina HumanHT-12 V4.0 expression beadchip |
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| Samples (46)
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| This SubSeries is part of SuperSeries: |
| GSE73237 |
Heterogeneity in global gene expression profiles between biopsy specimens taken peri-surgically from primary ER-positive breast carcinomas |
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| Relations |
| BioProject |
PRJNA296674 |
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