Cytoscantm hd array

The CNA genetic landscape of tumor samples before and after NAC was outlined using Affymetrix microarrays (Santa Clara, CA, USA) CytoScanTM HD Array (http://www.affymetrix.com/esearch/search.Jsp?Pd=prod520004&N=4294967292) in accordance with protocol. The GeneChip^® Scanner 3000 7G (Affymetrix) was used to read the chips, the Chromosome Analysis Suite 4.1 software (Affymetrix) was used to analyze the microarray data and determined losses and gains of chromosomal loci.

A microarray analysis was performed on high-density microarrays (DNA chips) of an Affymetrix (USA) CytoScan^TM HD Array to determine the presence of chromosomal aberrations of the BRCA1 gene. Sample preparation, hybridization, and scanning procedures were performed according to the manufacturer’s protocol of an Affymetrix GeneChip^® Scanner 3000 7G system (Affymetrix, Santa Clara, CA, USA). To process the results of microchipping, we used Chromosome Analysis Suite 4.0 (Affymetrix, Santa Clara, CA, USA) for the detection of aberrations—deletions or amplifications (losses or gains)—and loss of heterozygosity (LOH).

Microarray analysis on high-density microarrays from Affymetrix (USA) CytoScan^TM HD Array was used to evaluate the CNA performed, which contains 1 million 900 thousand non-polymorphic markers for the analysis of copy number aberrations. Sample preparation, hybridization, and scanning procedures were performed in accordance with the manufacturer’s protocol on the Affymetrix GeneChip^® Scanner 3000 7G system (Affymetrix, Santa Clara, CA, USA). CytoScan HD Suite has greater than 99% sensitivity and can reliably detect 25–50 kb copy number changes across the genome at high specificity (amplifications (gain) and deletions (loss) sections of chromosomes). Chromosome Analysis Suite 4.1 (Affymetrix, Santa Clara, CA, USA) was used for statistics. As a result of the analysis, amplifications (that is, an increase in the number of copies of the gene) and deletions (that is, a decrease in the number of copies of the gene) of the BRCA1, BRCA2, and PALB2 genes were determined.