Infinium genotyping data from paired FF and ligated FFPE samples of CRC and adjacent normal tissue. These samples are an independent set from those used for Infinium methylation. (A) The genotype call rates for ligated FFPE samples were significantly lower and more variable than those of the FF replicates. (B) Representative logR ratio (upper pane) and B-allele frequency (lower pane) from chromosome 1 from the FF sample from an individual patient (C_28) (C) Corresponding data for the FFPE replicate of the same patient in panel B, who had the higher call rate in FFPE sample. (D) Representative logR ratio and B-allele frequency plots from chromosome 18 from the FF sample from a second patient (C_34). (E) Corresponding data for the FFPE replicate from the same patient C_34 in panel D, who had lower call rates in FFPE sample.