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Appendix I: PCR Design

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posted on 2020-06-02, 10:00 authored by Ihthisham AliIhthisham Ali
PhD thesis: PRDM9 Diversity, Recombination Landscapes and Childhood Leukaemia by Ihthisham Ali

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.

A. DNA3 and AA hotspots
B. ALL K-ZnF Screening duplex PCR
C. PCR product for Sanger Sequencing PRDM9 ZnF array template
D. AA Hotspot ASP Design
E. AA Hotspot Universal Primer Design
F. DNA3 Hotspot Universal Primer Design
G. AA Hotspot Linkage Phasing
H. d257 (20) RC mapping resolved by plates and series

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