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For primers using a touchdown programme the annealing temperature was decreased by 1 °C each cycle for the first 10 cycles, starting from 65 °C.
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Thermal cycling was carried out with a TC-512 thermal cycler (Techne, Burlington, NJ) using a touchdown PCR program from 65°C to 55°C.
The amplification reactions were performed in the Rotor-Gene Q real-time PCR system (Qiagene, Germany) using a touchdown temperature profile (Table 2).
Multiple infections were also detectable using a touchdown approach.
The amplifications were conducted using a touchdown cycle [ 23].
Sixteen SSR loci (Table 3) were amplified as previously described [ 38, 42] using a touchdown PCR profile optimised for each set of primers: touchdown 60°C to 55°C or touchdown 55°C to 50°C.
All primer pairs were initially tested using a "touchdown 58" PCR protocol.
PCR products were generated using a touchdown PCR cycle with annealing temperatures decreasing 0.5°C per cycle from 68 to 60°C.
Of 26 breast tumors, 5 (19%) tested HPV positive by the standard assay and 15/26 (58%) using a touchdown protocol.
Briefly, 24 STR markers in regions showing loss of heterozygosity in cancer were amplified using a touchdown PCR protocol.
The reaction was run using a touchdown PCR protocol where the annealing temperature was started at 63°C and decreased for 0.5°C per cycle for 12 cycles.
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