Figure 2

SNPscanPlot visualizes data on SNP genotype and copy number. A. Screen capture of SNPscanPlot output for three cases (NA07055, NA07056, NA12874). Each SNP array data set is organized in a row; options for types of input are 10 K, 50 K (Hind or Xba), or 100 K (combined Hind and Xba) arrays. The x-axis spans chromosomes 1–22 and X, with centromeres indicated (grey rectangles; see panel B for enlarged view). Note that a male case (bottom row) is easily distinguished from female cases by the profile of the hemizygous X chromosome, including many homozygous calls (blue dots), significant LOH -log₁₀ p values (grey background), and a significant -log₁₀ p value for copy number changes (yellow background). Also of note are a deletion on chromosome 2 (top row, dashed circle) and a region of UPD across chromosome 1 (bottom row, dashed circle). B. SNPscanPlot allows an expanded view of any chromosome(s); 22 and X are shown for the cases in panel A, highlighting the differences observed between male and female X chromosome SNP profiles.