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Figure 2 | Human Genomics

Figure 2

From: Whole genome DNA copy number changes identified by high density oligonucleotide arrays

Figure 2

The results for 99 autosomal single nucleotide polymorphisms using the SK-BR-3 breast cancer cell line. The pairwise scatter-plots are based on three measurements: copy number, significance and the change in threshold cycle (Δ Ct). The significance measure is represented by the log 10 transformed p-value derived from the algorithm. To distinguish between deletions and amplifications, the -log10 (p -value) is used when the target value is higher than the reference mean, ie denoting amplification, and the log10 (p -value) is used when the target value is lower than the reference mean, ie denoting deletion. Copy number is estimated using the following formula: Copynumberexp ( 0 . 659 + 0 . 939 × ( S ̃ j g C - μ ^ j g ) ) . ΔCt denotes the difference between the normal DNA sample versus SK-BR-3. The Ct is the cycle number at which the reporter fluorescence passes a fixed threshold above baseline. Positive ΔCt suggests amplification, while negative ΔCt suggests deletion.

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