Validation of CNV using array CGH and fibre-FISH. a) The reference genomic region studied, showing the location of the sequences used in the paralogue ratio test (PRT) and the fosmids used for fibre-FISH analysis. b) Fibre-FISH analysis on stretched DNA fibres from three lymphoblastoid cell lines using the fosmid probes shown in part a). The three cell lines are from a YRI parent–child trio recruited for the HapMap project, with their DNA sample IDs given. PRT copy number estimates are given under each ID, and copy number estimated from each stretched individual chromosome given immediately to the left of a representative fiber-FISH image. c) Comparison of raw PRT estimates of CCL3L1 copy number on HapMap YRI samples (x-axis) with estimates from arrayCGH data (y-axis). Points are coloured according to final integer copy number estimates, as indicated by the key below the scatterplot. PC1=first principal component of arrayCGH data.