Fig. 2

Principles of Copy Number and B-allele Frequency Calculation and Presentation in the OncoScan Microarray Analysis a Copy number variations of gain, loss and copy-neutral loss of heterozygosity (LOH) are displayed in a segment of artificial chromosomes. Numbers mark the position of each single-nucleotide polymorphism (SNP). Blue and red lines represent chromosomes from father and mother, respectively. The gain region represented by SNP4 ~ 7 is generated by acquisition of additional mother’s chromosome segment. The loss region detected by SNP8 ~ 10 has a chromosome segment inherited only from father. The copy-neutral LOH indicated by SNP11 ~ 13 has duplicated father’s chromosome segments. Letter “A” stands for a major allele and letter “B” does for a minor allele. Genotypes of major (A) alleles are determined by the A/T OncoScan microarray, while those of minor (B) alleles are done by the G/C OncoScan microarray. Circles represent probes, and intensities of fluorescence signal are presented by different colors in the order of white color for no signal through orange and pink to red color for the greatest intensity in this presentation. b Copy number is determined by dividing the normalized signal intensities of sample at each probe by those of the reference at the corresponding probe. On homozygous probes, either A/T or G/C channel signal intensity is counted, while on heterozygous probes, signal intensities of both channels are included in the calculation. In the graph, it is displayed as a base 2 logarithm. Normal or seemingly normal of two copy numbers have zero values. Gain and loss have higher and lower values than zero, respectively. c B-allele frequency (BAF) is calculated by dividing the signal intensities of minor (B) allele by those of major (A) plus minor (B) alleles. In normal sample, three values of 1, 0.5, and 0 are obtained. A gain region generates four values (e.g., 0, 0.33, 0.67, and1) and it is interpreted as allelic imbalance. Loss and loss events followed by duplication such as uniparental disomy have LOH, and BAF at each probe has either 0 or 1 without intermediate values if the sample is homogeneous for cancer burden