Table 3. Genes involved in stem cell pluripotency, drug resistance, signal transduction or cancer development, recurrently amplified or deleted in the presence of MS-5.

Gene	Chromosome location	array-CGH experiment			Full name	Function
		imatinib	ponatinib	ponatinib
		F3 vs E5	A23 vs C9	A24 vs B4
CD274	9p24.1	loss	loss	loss	Programmed cell death 1 ligand 1 (PD-L1)	Transmembrane protein, role in immune response
CD58	1p13.1	loss	gain	gain	Lymphocyte function-associated antigen 3 (LFA-3)	Cell molecule adhesion
ECT2	3q26.31	gain	loss	loss	Epithelial cell transforming sequence 2 oncogene	Guanine nucleotide exchange factor, cell communication, signal transduction
TNFSF10	3q26.31	gain	loss	loss	TNF-related apoptosis-inducing ligand (TRAIL)	Receptor binding, cell communication, signal transduction
CDKN2A	9p21.3	(1)	gain	loss	Cyclin-dependent kinase inhibitor 2A (p14ARF)	Cell cycle control protein, cell communication, signal transduction
CCDC6	10q21.2	loss	(1)	loss	Coiled coil domain containing 6	Structural constituent of cytoskeleton, apoptosis
EXT1	8q24.11	(1)	gain	gain	Exostosin glycosyltransferase 1	Glycosyltransferase
FOXO3	6q21	gain	gain	(1)	Forkhead box protein O3A	Transcription factor activity
JAK2	9p24.1	loss	loss	(1)	Janus kinase 2	Protein-tyrosine kinase activity, cell communication, signal transduction
MLLT3	9p21.3	(1)	gain	loss	AF9, Mixed-Lineage Leukemia (Trithorax Homolog, Drosophila) Translocated To 3	Found in acute leukemias with MLL rearrangement
TMPRSS2	21q22.3	loss	loss	(1)	Transmembrane protease serine 2	Serine protease

For each array-CGH experiments, two resistant clones harboring the same mutation were compared (F3 vs E5, A23 vs C9, A24 vs B4). Clones F3, A23 and A24 were recovered from culture with MS-5 feeder. Clones E5, C9 and B4 were recovered from culture without MS-5 feeder. (1) no variation.