Examples of amplification and deletions together with genotyping data generated by the p501 array compared with BAC CGH data. (Top panel) The fluorescence ratio plot from the p501 array showing the smoothed fluorescent intensity data of the sample divided by the figure from the reference sample. (Second panel) The p-value plot for the individual SNPs calculated by comparison to the mean and standard deviation of 29 normal DNAs with deletions represented by red lines and amplifications in green. (Third and fourth panels) The genotypes for the tumor and matched normal samples, respectively; homozygous SNPs are represented by a red line below the center point whereas heterozygous markers are represented by a green line above the center point. (Bottom panel in C and D only) The results for BAC-array-based CGH (where available). (A) Genomic amplification at the C-MYC locus (arrow) on Chromosome 8 in the prostate line COR-L96-CAR. (B) A homozygous deletion (arrow) at the p16/INK4 locus on Chromosome 9 in the renal cell carcinoma cell line LB1047. (C) Chromosome 18 from the breast cancer cell line HCC1937. (i) This chromosome has a copy number of 2 (intensity ratio of 1) from the pter until 18q12.1. (ii) The copy number drops to 1 (intensity ratio of 0.5) from 18q12.1 until the 18qter, although the genotyping data indicate that this line is heterozygous across the full length of Chromosome 18. (D) Chromosome 5 from the small cell lung cancer line NCI-H209. This chromosome shows a complex pattern with partial amplification of the p-arm (i), followed by a drop in fluorescent intensity to 0.5 with corresponding LOH determined from the genotyping data (ii), until 5q23.2 (iii), where the intensity ratio recovers to 1 (copy number of 2); however, this region still represents LOH as determined by the genotyping data and therefore represents duplication of a single parental chromosome. There is also a homozygous deletion at 5q14.3 (arrow). This was not detected with the BAC array, as the array does not have a clone that covers this region.
