Infinium humancytosnp 12v2.1 beadchip

Extracted DNA was adjusted to a concentration of 50 ng/μL. All 92 paired samples were assayed using the Infinium HumanCytoSNP‐12v2.1 BeadChip (Illumina, San Diego, CA), which contains 299,140 single nucleotide polymorphism (SNP) loci, according to the Illumina Infinium HD assay protocol. BeadChips were scanned using iScan (Illumina) and analyzed using GenomeStudio software (v.2011.1; Illumina). The log R ratio (LRR) and B allele frequency (BAF) for each sample were exported from normalized Illumina data using GenomeStudio. Data analysis was carried out using KaryoStudio 1.4.3 (CNV Plugin v3.0.7.0; Illumina) with default parameters. CNAs were classified as described below. In the classification of chromosome copy number alterations by CNA partition algorithms, LRR 0 indicated a normal diploid region, LRR > 0 indicated a copy number gain and LRR < 0 indicated a copy number loss‐of‐heterozygosity (LOH). BAF values ranged from 0 to 1; homozygous SNPs had BAFs near 0 (A‐allele) or 1 (B‐allele), and heterozygous diploid region SNPs had BAFs near 0.5 (AB genotype). Additionally, LRR and BAF data were used to identify regions of hemizygous and copy‐neutral LOH.

Extracted DNA was adjusted to a concentration of 50 ng/µL. All 106 paired samples were assayed using an Infinium HumanCytoSNP‐12v2.1 BeadChip (Illumina, San Diego, CA), which contains 299 140 single nucleotide polymorphism (SNP) loci, according to the Illumina Infinium HD assay protocol.12 BeadChips were scanned using iScan (Illumina) and analyzed using GenomeStudio software (v.2011.1; Illumina). The log R ratio (LRR) and B allele frequency (BAF) for each sample were exported from normalized Illumina data using GenomeStudio. Data analysis was performed using KaryoStudio 1.4.3 (CNV Plugin v3.0.7.0; Illumina) with default parameters. CNVs were classified as described below. In the classification of chromosome copy number variations by CNV partition algorithms, LRR 0 indicated a normal diploid region, LRR greater than 0 indicated a copy number gain, and LRR less than 0 indicated a copy number loss‐of‐heterozygosity (LOH). BAF values ranged from 0 to 1; homozygous SNPs had BAFs near 0 (A‐allele) or 1 (B‐allele), and heterozygous diploid region SNPs had BAFs near 0.5 (AB genotype). Additionally, LRR and BAF data were used to identify regions of hemizygous and copy‐neutral LOH.
In the present study, we classified copy number alterations into three types, including copy number gains (CN‐gains), copy number‐loss of heterozygosity (LOH), and copy neutral‐LOH.12