The intention was to detect genes that are determining trastuzumab efficiency in HER2-positive breast cancer cell lines with different resistance phenotypes.;	While BT474 should be sensitive to the drug treatment, HCC1954 is expected to be resistant due to a PI3K mutation.;	The cell line BTR50 has been derived from BT474 and was cultured to be resistant as well.;	Based on RNA-Seq data, we performed differential expression analyses on these breast cancer cell lines with and without trastuzumab treatment.;	In detail, five separate tests were performed, namely resistant cells vs. wild type, i.e. HCC1954 and BTR50 vs. BT474, respectively, and untreated vs. drug treated cells.;	The significant genes of the first two tests should contribute to resistance.;	The significant genes of the test BT474 vs. its drug treated version should contribute to the trastuzumab effect.;	To exclude false positives from the combined gene set (#64), we removed ten genes that were also significant in the test BTR50 vs. its drug treated version.;	This way we ended up with 54 genes that are very likely to determine trastuzumab efficiency in HER2-positive breast cancer cell lines. SOURCE: Silvia von der Heyde (silvia.heyde@gmail.com) -  University Medical Center Göttingen

Pluto Bioinformatics

GSE55005: mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer