Agilent whole human 44k genome oligo array

Sixty primary tumor samples were obtained from patients who had surgical resection of a GIST, and patients were followed without treatment until tumors recurred as previously described [33 (link)]. Frozen samples from resected primary GISTs untreated until tumor recurrence were selected from the European GIST database CONTICAGIST (http://www.conticagist.org). According to French law at the time of the study, experiments were performed in agreement with the Bioethics Law 2004 800 and the Ethics Charter from the National Institute of Cancer; all subjects signed a non-opposition statement for research use of their sample. Total RNA was extracted from each frozen tumor sample, and analyzed on Agilent Whole human 44K Genome Oligo Array (Agilent Technologies) as previously described [33 (link)]. Patient characteristics were previously described [33 (link)]. These data were kindly provided by Dr. F. Chibon, Institute Bergonie, Bordeaux, France.

According to the manufacturer's procedures, the 387 complex genetics sarcomas were analyzed on Human Genome U133 Plus 2.0 array (900466, Affymetrix, Santa Clara, CA, USA). For GIST, synovial sarcomas, LPS, and 87 complex genetics sarcomas, gene expression analysis was carried out by Agilent Whole Human 44K Genome Oligo Array (G4112A, Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s protocol.

Gene expression analysis was carried out using Agilent Whole human 44 K Genome Oligo Array (Agilent Technologies) according to the manufacturer’s protocol. All microarrays were simultaneously normalized using the Quantile algorithm. T-tests were performed using Genespring (Agilent Technologies) and P-values were adjusted using the Benjamini-Hochberg procedure. The P-value and fold change cut-off for gene selection were 0.001 and 2, respectively. Gene ontology (GO) analysis was performed to establish statistical enrichment in GO terms using Genespring (Agilent Technologies). Heatmap and boxplot were performed using with R (v3.6.2). The datasets generated and analyzed are available at the GEO, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171471.