DNA from fresh frozen tissue was isolated using the wizard genomic DNA purification kit (Promega, Madison, WI), according to the manufacturer instructions.
Label
biotin
Label protocol
Genomic DNA preparation, labeling and hybridization were performed according to Affymetrix's recommended protocols (Affymetrix, Santa Clara, CA, USA).
Hybridization protocol
Genomic DNA preparation, labeling and hybridization were performed according to Affymetrix's recommended protocols (Affymetrix, Santa Clara, CA, USA).
Scan protocol
Arrays were scanned with GeneChip GSC3000 7G Whole-Genome Association System (Affymetrix).
Description
High-grade osteosarcoma pre-chemotherapy biopsy Affymetrix SNP 6.0 arrays were used.
Data processing
Microarray data pre-processing was performed as described in Pansuriya et al. (PMID: 21235737). Hybridization quality was estimated by the genotype call rate using the Birdseed genotype calling algorithm in Genotyping Console (version 4.0, Affymetrix). We performed copy number analysis in Nexus software version 5 using CNCHP log-ratio files generated by genotyping console using 27 controls as a baseline, which is a subset of the reference set of 29 samples which was used in Pansuriya et al (PMID: 21235737, GEO Series accession number GSE22984), because we rejected 2 samples based on results from the quality control analysis in Genotyping Console. We used the following samples for the reference file (GEO accession numbers): GSM566679, GSM566716, GSM566745, GSM566752, GSM566762, GSM566780, GSM566785, GSM566787, GSM566788, GSM566789, GSM566790, GSM566791, GSM566814, GSM566815, GSM567029, GSM567042, GSM567046, GSM567050, GSM567053, GSM567055, GSM567062, GSM567083, GSM567110, GSM567114, GSM567339, GSM567342, GSM567343. Hidden Markov model (HMM) based SNP-FASST segmentation was used to identify aberrant genomic regions. We used an aberration frequency cut-off of 35%.
