TY - JOUR
T1 - Use of formalin-fixed paraffin-embedded samples for gene expression studies in breast cancer patients
AU - Musella, Valeria
AU - Callari, Maurizio
AU - Di Buduo, Eleonora
AU - Scuro, Manuela
AU - Dugo, Matteo
AU - Miodini, Patrizia
AU - Bianchini, Giampaolo
AU - Paolini, Biagio
AU - Gianni, Luca
AU - Daidone, Maria Grazia
AU - Cappelletti, Vera
PY - 2015/4/6
Y1 - 2015/4/6
N2 - To obtain gene expression profiles from samples collected in clinical trials, we conducted a pilot study to assess feasibility and estimate sample attrition rates when profiling formalinfixed, paraffin-embedded specimens. Ten matched fresh-frozen and fixed breast cancer samples were profiled using the Illumina HT-12 and Ref-8 chips, respectively. The profiles obtained with Ref 8, were neither technically nor biologically reliable since they failed to yield the expected separation between estrogen receptor positive and negative samples. With the use of Affymetrix HG-U133 2.0 Plus chips on fixed samples and a quantitative polymerase chain reaction -based sample pre-assessment step, results were satisfactory in terms of biological reliability, despite the low number of present calls (M = 21%±5). Compared with the Illumina DASL WG platform, Affymetrix data showed a wider interquartile range (1.32 vs 0.57, P
AB - To obtain gene expression profiles from samples collected in clinical trials, we conducted a pilot study to assess feasibility and estimate sample attrition rates when profiling formalinfixed, paraffin-embedded specimens. Ten matched fresh-frozen and fixed breast cancer samples were profiled using the Illumina HT-12 and Ref-8 chips, respectively. The profiles obtained with Ref 8, were neither technically nor biologically reliable since they failed to yield the expected separation between estrogen receptor positive and negative samples. With the use of Affymetrix HG-U133 2.0 Plus chips on fixed samples and a quantitative polymerase chain reaction -based sample pre-assessment step, results were satisfactory in terms of biological reliability, despite the low number of present calls (M = 21%±5). Compared with the Illumina DASL WG platform, Affymetrix data showed a wider interquartile range (1.32 vs 0.57, P
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U2 - 10.1371/journal.pone.0123194
DO - 10.1371/journal.pone.0123194
M3 - Article
AN - SCOPUS:84927562842
SN - 1932-6203
VL - 10
JO - PLoS One
JF - PLoS One
IS - 4
M1 - e123194
ER -