## Additional file 1: of An integrated analysis tool for analyzing hybridization intensities and genotypes using new-generation population-optimized human arrays

2016-03-31T05:00:00Z (GMT) by
A whole-genome six-panel figure of the fifth sample in Fig. 3, which is genotyped using Axiom. This figure depicts the AF, AI, LOH/LCSH, and CNV/CNA analyses provided by ALICE. From top to bottom, the six-panel plot consists of the AF plot, AI plot, LOH/LCSH plot, HI and CN segmentation plot, proportion plot of CNV/CNA, and statistical significance plot of CNV/CNA. The details of each panel are described as follows: (1) In the AF plot, the vertical axis is the estimated AF, ranging from 0 to 1, and the horizontal axis is the physical position (Mb) on a chromosome. Each point denotes a SNP probe; blue and red points indicate non-AI and AI SNPs, respectively. (2) In the AI plot, the vertical axis is the proportion of AI SNPs, ranging from 0 to 1, and the horizontal axis is the physical position (Mb) on a chromosome. The light-red (deep-red) curve indicates the proportion of AI SNPs in sliding windows for the sample before (after) a smoothing spline. The light-blue (deep-blue) curve indicates the 95 % quantile of the proportions of AI SNPs in sliding windows for normal control samples before (after) a smoothing spline. The red bar at the top of the AI plot signifies a region of AI; thus, the deep-red curve is higher than the deep-blue curve. The deeper the red color in the bar, the higher is the proportion of AI SNPs in sliding windows. (3) In the LOH/LCSH plot, the vertical axis is the proportion of LOH/LCSH SNPs, ranging from 0 to 1, and the horizontal axis is the physical position (Mb) on a chromosome. The light-red (deep-red) curve indicates the proportion of LOH/LCSH SNPs in sliding windows for the sample before (after) a smoothing spline. The light-blue (deep-blue) curve indicates the 95 % quantile of the proportion of LOH/LCSH SNPs in sliding windows for normal control samples before (after) a smoothing spline. The red bar at the top of the LOH/LCSH plot signifies a region of LOH/LCSH; thus, the deep-red curve is higher than the deep-blue curve. The deeper the red color in the bar, the higher is the proportion of LOH/LCSH SNPs in sliding windows. (4) In the HI and CN segmentation plot, the vertical axis is the HI value, and the horizontal axis is the physical position (Mb) on a chromosome. Each point denotes a SNP probe (or a CN probe in Array 6.0); a light-blue point indicates the HI value of a marker, and a deep-blue point indicates the HI value of an AI SNP. Red and green segments obtained from the circular binary algorithm indicate segments of CN gain and loss, respectively. (5) In the proportion plot of CNV/CNA, the vertical axis is the proportion of CNV/CNA, ranging from 0 to 1, and the horizontal axis is the physical position (Mb) on a chromosome. Each point denotes a SNP probe (or a CN probe in Array 6.0). The light-red (deep-red) curve indicates the proportion of CN gain in sliding windows for the sample before (after) a smoothing spline. The light-green (deep-green) curve indicates the proportion of CN loss in sliding windows for the sample before (after) a smoothing spline. The light-blue (deep-blue) curve indicates the 95 % quantile of the proportions of CNV/CNA in sliding windows for normal control samples before (after) a smoothing spline. The green (red) bar at the top of this plot signifies a region that satisfies the following criteria: a) the proportion of CN loss (gain) in the sample is higher than that in the normal reference samples and b) p value of this region is statistically significant. The deeper the green (red) color in the bar, the higher is the proportion of CN loss (gain) in sliding windows. (6) In the statistical significance plot of CNV/CNA, the vertical axis is the adjusted p value (in a scale of − log10), and the horizontal axis is the physical position (Mb) on a chromosome. Each point denotes a SNP probe (or a CN probe in Array 6.0); a gray point represents the p value of a probe from a single-point association analysis. A blue point represents the p value from a multipoint association analysis, and the p value does not reach statistical significance. A green (red) point indicates a p value from a multipoint association analysis, and the p value reaches statistical significance of CN loss (gain). The green (red) bar at the top of this plot signifies a region that satisfies the following criteria: a) the proportion of CN loss (gain) in the sample is higher than that in the normal reference samples and (b) p value of this region is statistically significant. The deeper the green (red) color in the bar, the higher is the p value (in a scale of − log10) of CN loss (gain) in sliding windows. (TIFF 857 kb)