Emulsion haplotype fusion PCR. Two loci, approximately 12kb apart are illustrated. Locus 1 corresponds to a single-copy region flanking the copy number variable region containing DEFA1A3 (locus 2). DEFA1A3 repeat units are illustrated as arrows, with a black arrow representing the most telomeric repeat, and a grey half arrow representing another repeat unit present to the right. Amplicons to be fused are shown in A-D: A. Independent amplification occurs at locus 1 and locus 2, with primers F1, F2’R1 and R2 used in the emulsion. Primer F2 is shown in light grey, and is not used in the emulsion but is necessary for the design of the tailed primer B. Locus 1 amplicon primes on locus 2, creating the fusion product. C. Fused product is amplified with F1 and R2. D. Allele-specific PCR (ASPCR) with nested primers allows determination of each haplotype by sequencing.
Tyson and Armour BMC Genomics 2012 13:693 doi:10.1186/1471-2164-13-693