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| Status |
Public on Sep 05, 2018 |
| Title |
Feasibility of Developing Reliable Gene Expression Modules from FFPE Derived RNA Profiled on Affymetrix Arrays |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
This SuperSeries is composed of the SubSeries listed below.
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 |
Refer to individual Series
Using eight breast cancer tumors with available frozen and FFPE samples, five sample-matched data sets were generated from different combination of arrays , amplification-and-labeling kit and sample preservation method as listed below; 1) Two data set from matched FFPE and frozen samples profiled on HG-U133plus2 arrays with Affymetrix's 3'IVT kit (u133p2.3ivt array / 3ivt kit), 2) Two data set from matched FFPE and frozen samples profiled on HG-U219 arrays with Nugen's Ovation® FFPE WTA System and EncoreTM Biotin Module (u219.ovation arrays / ovation kit), and 3) a single data set from matched FFPE samples profiled on HG-U219 arrays with Affymetrix's SensationPlusTM FFPE Amplification and 3'IVT Labeling Kit (u219.sensation array / sensation kit). We consider the data set which profiled frozen samples on HG-U133plus2 array with 3'IVT kit as 100% truth and compared all other data sets to this reference data set. The eight BC tumors include two tumors from each Luminal-A, Luminal-B, HER2-amplified and Triple-Negative subtypes
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| Citation(s) |
30169535 |
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| 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 (2) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
| GPL13667 |
[HG-U219] Affymetrix Human Genome U219 Array |
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| Samples (40)
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| GSM2451624 |
sample4, dataset1 |
| GSM2451625 |
sample5, dataset1 |
| GSM2451626 |
sample6, dataset1 |
| GSM2451627 |
sample7, dataset1 |
| GSM2451628 |
sample8, dataset1 |
| GSM2451629 |
sample1, dataset2 |
| GSM2451630 |
sample2, dataset2 |
| GSM2451631 |
sample3, dataset2 |
| GSM2451632 |
sample4, dataset2 |
| GSM2451633 |
sample5, dataset2 |
| GSM2451634 |
sample6, dataset2 |
| GSM2451635 |
sample7, dataset2 |
| GSM2451636 |
sample8, dataset2 |
| GSM2451637 |
sample1, dataset3 |
| GSM2451638 |
sample2, dataset3 |
| GSM2451639 |
sample3, dataset3 |
| GSM2451640 |
sample4, dataset3 |
| GSM2451641 |
sample5, dataset3 |
| GSM2451642 |
sample6, dataset3 |
| GSM2451643 |
sample7, dataset3 |
| GSM2451644 |
sample8, dataset3 |
| GSM2451645 |
sample1, dataset4 |
| GSM2451646 |
sample2, dataset4 |
| GSM2451647 |
sample3, dataset4 |
| GSM2451648 |
sample4, dataset4 |
| GSM2451649 |
sample5, dataset4 |
| GSM2451650 |
sample6, dataset4 |
| GSM2451651 |
sample7, dataset4 |
| GSM2451652 |
sample8, dataset4 |
| GSM2451653 |
sample1, dataset5 |
| GSM2451654 |
sample2, dataset5 |
| GSM2451655 |
sample3, dataset5 |
| GSM2451656 |
sample4, dataset5 |
| GSM2451657 |
sample5, dataset5 |
| GSM2451658 |
sample6, dataset5 |
| GSM2451659 |
sample7, dataset5 |
| GSM2451660 |
sample8, dataset5 |
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| This SuperSeries is composed of the following SubSeries:
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| GSE93332 |
Fresh-Frozen samples profiled on HG-U133plus2 array with Affymetrix's GeneChip® 3' IVT Express kit |
| GSE93334 |
FFPE samples profiled on HG-U133plus2 array with Affymetrix's GeneChip® 3' IVT Express kit |
| GSE93335 |
Fresh-Frozen samples profiled on HG-U219 array with Nugen's Ovation® FFPE WTA System and EncoreTM Biotin Module [dataset 3] |
| GSE93336 |
FFPE samples profiled on HG-U219 array with Nugen's Ovation® FFPE WTA System and EncoreTM Biotin Module |
| GSE93337 |
FFPE samples profiled on HG-U219 array with Affymetrix's SensationPlusTM FFPE Amplification and 3'IVT Labeling kit |
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| Relations |
| BioProject |
PRJNA360624 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE93338_RAW.tar |
110.6 Mb |
(http)(custom) |
TAR (of CEL) |
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