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. 2015 May 4;7(1):42. doi: 10.1186/s13073-015-0148-0

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© Lin et al.; licensee BioMed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Schematic of primer design for haplotype phasing of SNP genotypes in relation to the ~11 kb APC 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.