Feature extraction version software

DNA was extracted from a peripheral blood sample of the patient using QIAsymphony DSP DNA Kits according to the manufacturer's instructions. Genome‐wide copy number analysis was performed using an Affymetrix CytoScan 750K Array according to the manufacturer's instructions. Regions of copy number change were determined using the Affymetrix Chromosome Analysis Suite software (ChAS) v.3.2 and interpreted with the aid of the UCSC genome browser (http://genome.ucsc.edu/; Human February 2009 GRCh37/hg19 assembly).
In the case of parental samples, 1 μg of DNA and opposite‐sex commercially available control DNA were labeled with Cy3‐ or Cy5‐deoxycytidine triphosphate, respectively, using Exo‐Klenow (OGT Cytosure Labeling Kit, catalogue no. 020020), and hybridized to a CytoSure ISCA 8 × 60 k array at 65°C for 18 hr. The array was washed and scanned with the Agilent High‐Resolution Microarray Scanner Model G2505B at 3‐µm resolution. Data analysis was performed using Feature Extraction version software from Agilent technologies and CytoSure Interpret Software (OGT).

Expression levels of miRNAs isolated from plasma and tissue samples were assessed by SurePrint G3 Human miRNA Microarrays (8 × 60 k, Release 21.0, Design ID 070156; Agilent Technologies, Santa Clara, CA, USA) according to manufacturers’ protocol. Plasma levels of miRNA are generally low and thus the volume of the sampled plasma was used to standardize sample amount used for subsequent analyses. Briefly, 3.1 µL of total RNA isolated from plasma samples or 2 µL of total RNA (50 ng/µL) isolated from tumor samples was labeled with Cy3 using the miRNA Complete Labeling and Hybridization Kit and spiked with synthetic control miRNAs for accessing labeling performance (Agilent Technologies). The Cy3-labeled samples were hybridized for 20 h at 55 °C in a rotator oven. After washing steps, the array slides were scanned using AgilentSureScan microarray scanner (Agilent Technologies). Expression data and Quality Control (QC) Reports were extracted from the scanned images using Feature Extraction version software (version 12.1, Agilent Technologies). The data generated in this study are publicly available in Gene Expression Omnibus (GEO) at GSE205027.