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Series GSE93334 Query DataSets for GSE93334
Status Public on Sep 05, 2018
Title FFPE samples profiled on HG-U133plus2 array with Affymetrix's GeneChip® 3' IVT Express kit
Organism Homo sapiens
Experiment type Expression profiling by array
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.
 
Overall design RNA were extracted from eight FFPE 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.
 
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) vinu.jose@yahoo.co.in
Organization name Institut Jules Bordet – Université Libre de Bruxelles (ULB)
Lab Breast Cancer Translational Research Laboratory J.C. Heuson (ULB 290)
Street address Rue Meylemeersch 90
City Brussels
ZIP/Postal code 1070
Country Belgium
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (8)
GSM2451629 sample1, dataset2
GSM2451630 sample2, dataset2
GSM2451631 sample3, dataset2
This SubSeries is part of SuperSeries:
GSE93338 Feasibility of Developing Reliable Gene Expression Modules from FFPE Derived RNA Profiled on Affymetrix Arrays
Relations
BioProject PRJNA360634

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE93334_RAW.tar 28.1 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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