Combined Analysis with Copy Number Variation Identifies Risk Loci in Lung Cancer
Figure 1
CNV associations regarding amplification are related to recombination hotspot regions in EAGLE and PLCO. The −log 10 ( value) in the (a) Pearson testing and (b) Gain testing are plotted against the corresponding log 10 (relative factors). The SNP sites above a significant level (combining value and relative factor to ensure that the final false positive is less than 1) are in red. (c) The log 10 (maximum recombination rate) around the SNP sites (in 10 kb) are summed in four categories: not sig. (nonsignificant SNP sites), SNP-based (significant SNP sites that passed SNP-based testing), window (significant SNP sites that passed window-based testing), and window_Rf (risk loci that passed both window-based and combined testing). The log 10 (maximum recombination rate) is prevalent in the category of window_Rf ( value < 0.00001). (d) Most of these risk loci were located around recombination hotspots (plotted in gray lines and with peaks indicating the recombination rates). One of these associated sites, rs13381870, was arbitrarily chosen and is shown here as an example. The –log 10 ( value) of SNP sites in three hypotheses models (loss, abnm., and gain) in SNP-based testing are plotted in blue, orange, and red, respectively. Grey vertical lines show the high recombination rate sites. Hotspots from HapMap were shown as purple bars between the plot and genes. The names of genes around rs13381870 are shown in the figure.
