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| Status |
Public on Sep 05, 2018 |
| Title |
Fresh-Frozen samples profiled on HG-U133plus2 array with Affymetrix's GeneChip® 3' IVT Express kit |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
The reliability of differential expression analysis on FFPE expression profiles from Affymetrix arrays is questionable, due to the wide range of percent-present values reported in studies which profiled FFPE samples on Affymetrix arrays. Moreover the validity of externally defined gene-modules in FFPE microarray expression profiles is unknown. Using eight breast cancer tumors with available frozen and FFPE samples, five sample-matched data sets were generated from different combination of Affymetrix arrays, amplification-and-labeling kit and sample preservation method. The reliability of differential expression analysis was investigated by developing de novo ER/HER2 pathway gene-modules from matched data sets and validating it on external data set using ROC analysis. Spearman's rank correlation coefficient of module scores between matched FFPE-frozen expression profiles was used to measure reliability of externally defined gene-modules in FFPE expression profiles. Independent of array/amplification-kit/sample preservation method used, de novo ER/HER2 gene-modules derived from all matching data sets showed similar prediction performance during independent validation (AUC range; ER: 0.92-0.95, HER2: 0.88-0.91), except for de novo HER2 gene-module derived from FFPE data set with 3'IVT kit (AUC: 0.67-0.72). Further not all gene-module based biological signals present in frozen expression profiles can be recovered from matching FFPE microarray expression profiles using the currently available FFPE specific sample preparation kits. The gene-module based biological signal extracted from FFPE RNA, using microarrays, may not be as reliable as that from their frozen counterpart, if the sample preparation protocol used with FFPE RNA failed to recover relevant genes involved in the biological signal.
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| Overall design |
RNAs were extracted from eight Fresh-Frozen preserved breast cancers. RNAs were amplified and labeled using Affymetrix's GeneChip® 3' IVT Express kit, and profiled on Affymetrix's GeneChip® HG-U133 Plus2.0 Array according to Affymetrix's standard procedure.
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| Contributor(s) |
Jose V, Fumagalli D, Rothé F, Majjaj S, Loi S, Michiels S, Sotiriou C |
| Citation(s) |
30169535 |
| |
| Submission date |
Jan 09, 2017 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Vinu Jose |
| E-mail(s) |
[email protected]
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| Organization name |
Institut Jules Bordet – Université Libre de Bruxelles (ULB)
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| Lab |
Breast Cancer Translational Research Laboratory J.C. Heuson (ULB 290)
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| Street address |
Rue Meylemeersch 90
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| City |
Brussels |
| ZIP/Postal code |
1070 |
| Country |
Belgium |
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| Platforms (1) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE93338 |
Feasibility of Developing Reliable Gene Expression Modules from FFPE Derived RNA Profiled on Affymetrix Arrays |
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| Relations |
| BioProject |
PRJNA360635 |
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