Figure 2.

The LOH and MCP data views of a chromosome. The tumor samples are displayed on columns and the SNPs are ordered on rows by their chromosome positions. (A) Observed LOH calls by comparing normal (N) and tumor (T) genotypes at the same SNP. Yellow: retention (AB in both N and T), Blue: LOH (AB in N, AA or BB in T), Red: Conflict (AA/BB in N, BB/AA or AB in T), Gray: Non-informative (AA/BB in both N and T), White: No Call (No Call in N or T). (B) In the inferred MCP data view, the white and gray colors represent inferred MCP levels from 0.5 to 1 according to the color scale. When the inferred major copy allele is estimated to be different from the minor copy allele at a SNP (see "Methods"), the SNP position is colored in red or blue according to the major copy allele (A or B).