Appendix I: PCR Design
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PhD thesis: PRDM9 Diversity, Recombination Landscapes and Childhood Leukaemia by Ihthisham Ali <br><br>This appendix includes PCR designs for the recombination hotspot crossover assays done in the DNA3 and newly described AA hotspots in the MHCII, duplex PCR for screening for K-ZnF containing PRDM9 alleles in a British ALL cohort and Sanger sequencing as carried out in this thesis. PCR primer characteristics, PCR cycling conditions, PCR strategy for target regions and sequence context of target regions, AA hotspot morphology analysis are included. <br>A. DNA3 and AA hotspotsB. ALL K-ZnF Screening duplex PCRC. PCR product for Sanger Sequencing PRDM9 ZnF array templateD. AA Hotspot ASP DesignE. AA Hotspot Universal Primer DesignF. DNA3 Hotspot Universal Primer DesignG. AA Hotspot Linkage PhasingH. d257 (20) RC mapping resolved by plates and series
