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Figure 9 | BMC Bioinformatics

Figure 9

From: Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan

Figure 9

SNPscan result for three apparently normal individuals using 100 K data. SNPscan was used to analyze 100 K SNP data, combined from Affymetrix's 50 K Hind and 50 K Xba via CNAT v2.0. The first three tracks are a trio (father, NA11839; mother, NA11840; daughter, NA10854). Note that for both of the first two tracks, the patterns observed on the X chromosome are atypical. The first two tracks show a unique and apparently abnormal pattern of red dots in the copy number range that is normal for females (1–3), with blue dots exposed in a lowered copy number range that is normal for males (1–2). The p values (yellow area) for the first track are much higher than that of the second track, presumably because of the smaller number of heterozygous calls derived from the Hind array (see Table 3). Together, these observations suggest a pattern of SNPs that represents a combined male and female profile; our interpretation is that the labels were switched on two of the Hind datasets (see Table 3). The third track, showing data on an apparently normal female, has another pattern: many red and green dots mostly in the copy number range of 1 to 2.5, with p values (yellow) intermediate between normal female and male values. This represents a female with a mosaic loss of the X chromosome. After the labeling error was corrected for the first two tracks, the results (NA11839 as male and NA11840 as female) were plotted in the last two tracks.

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