Representative array-CGH log ratio plots of 2 DLBCL specimens (1664 and 939) using the 1-Mbp and 2- to 4-Mbp resolution arrays, respectively. (A) Custom normalization was performed, and an averaged log ratio for each clone was calculated for the duplicate forward and reverse hybridizations for each clone. Clones are organized according to linear chromosome position. For the 1-Mbp resolution array exemplified by specimen 1664, normalized log ratios are shown for 2436 autosomal clones. For the 2- to 4-Mbp resolution array exemplified by specimen 939, normalized log ratios are shown for 1421 autosomal clones. (B) CBS analysis identified segments (minimum of 2 contiguous clones) with the same distribution of ratios. (C) Constrained CBS analysis then defined segments of normal copy number (log ratio, approximately 0) compared with those of gain (log ratio, greater than 0) or loss (log ratio, less than 0) of copy number. Horizontal bars on the top and bottom of panel C show the gains and losses, respectively, of the specimen determined by chromosomal-CGH. Circled clones represent singleton clones (within CBS-defined segments of normal copy number) with a log ratio more than 3 SDs from the expected normal value and considered singleton genomic gain or loss.