Figure 2

Examples of loss events detected by segmentation analysis [22] in two Yoruba DNAs, NA19132 and NA19101, at putative CNV locus_id 3262. PCR across the putative breakpoint of the events showed truncated bands from both DNAs, which were excised and sequenced. The sequences of the truncated amplicons were mapped on build 36 to determine the precise breakpoints, which corresponded to identical 815-bp deletions in both DNAs. Although the homozygous deletion in NA19132 was detected on the genome-scan arrays, the one copy loss in NA19101 was missed. The red lines in the log2 ratio plots indicate the segments detected by CBS. Although not shown, the results from the a- and c- genome-scan arrays were nearly identical to the b-design. The events in both DNAs, however, were detected on the CNV-typing array. The CNV-typing array showed no events in the preceding CNV locus_id, 3261, approximately 350 kb upstream on chromosome 9. The log2 ratio (y-axis) scales are different between the genome-scan array and CNV-typing array, and reflect a higher response in the latter.