Schematic of primer design for haplotype phasing of SNP genotypes in relation to the ~11 kb
deletion. The primer pairs P14/P15 and P8/P13 flanked the ~11 kb deletion and relevant SNPs. Only amplification of the APC allele with the ~11 kb deletion would result in an amplicon A size of 5.5 kb and an amplicon B size of 6.9 kb. Amplification of the allele without the ~11 kb deletion would not be efficient, as the resultant amplicons would be greater than 16 kb. Amplicons A and B were used as templates for Sanger sequencing reactions to reveal polymorphic variations in the diagrammed SNPs flanking the ~11 kb deletion.