Comparison of the three methods used for studying gene copy number.

Gene copy number was measured using three methods, qPCR, aCGH and FISH. All samples used in this study had qPCR data and subset data for the other two methods. All available data were pooled and used for analysis of concordance and kappa statistics. All three comparisons show high concordance with low p values. Kappa analyses were used to determine the optimal cut-off value for each test. These analyses yielded the following cut-off values for determining copy number gains: qPCR��4.0, aCGH��3.0 and for FISH��4.5. Using these cut-off values, samples were scored as positive or negative for copy number gains for each type of test, and Fishers two sided tests were used for comparisons of the different tests.