Overall, the banding patterns we observed by unblot of WGA-DNA were in close agreement with those predicted by in silico restriction analysis of the Hg19 genome build (Figure 2A and B), implying uniform amplification of all regions of the DNA. On average, we observed between 18 and 22 bands per lane in fragments that varied from sample to sample. To further characterize the fragments observed to be polymorphic among individuals, we compared the distribution of polymorphic HML-2 proviruses with that of previously described copies, as interpreted by PCR screen. Comparison between HML-2derived unblotting and PCR **data** allowed for the provisional assignment of a few fragments based on shared distribution between each analysis, each of which was further supported in agreement with the corresponding in silico predicted sizes (asterisks in Figure 2A). Most clearly represented were the fragments predicted to represent the 11q22.1 5'LTR junction, with a band around 2.1 kb that Figure 2 Distribution of polymorphic HML-2 proviruses in breast cancer cases and controls. A. Comparative schematic representing the in silico-predicted sizes for HML-2 containing fragments following BsrI digestion and detected by the K-seq probe within the Hg19 genome build. Asterisks at left indicate the confirmed polymorphic proviruses, whose distribution coincides exactly between unblot banding patterns and PCR data. B. CPSII samples were sorted by case/control status (n = 25 each) and BsrI digested WGA-DNA from each group was separated by gel electrophoresis and probed with the 32 P-radiolabeled K-seq oligonucleotide. HML-2 junction fragments were visualized following exposure to film, and polymorphic insertions inferred by variable banding patterns among samples. C. Results from PCR analysis of known polymorphic proviruses for direct comparison of described polymorphic elements, where '+' indicates the confirmed presence of the tested provirus. Novel polymorphic fragments whose identity could not be inferred by comparison to PCR analysis or in silico predictions, have been indicated with arrows at right. Asterisks (at right) are used to indicate the observed fragment sizes of polymorphic elements detected in ≤5% individuals screened here.