Modified allele-specific PCR improves HER2 Ile655Val detection by reducing genotyping errors

Applied Cancer Research

Table 3 Effects of PCR-related factors on genotyping errors of HER2I655V AS-PCR for AG genotype

Type of error		DNA template ratio (w/w)^a										Annealing temperature (°C)^b
		A:G		A:G		A:G		A:G		A:G		51.1		57.7
		1:1		1:0.25		0.25:1		0.5:0.5		0.25:0.25		51.1		57.7
Experiments		1^th	2^nd	1^th	2^nd	1^th	2^nd	1^th	2^nd	1^th	2^nd	1^th	2^nd	1^th	2^nd
LDO	No PCR product	0	0	0	0	1	0	0	0	2	1	1	2	0	0
ADO	AA genotype only	0	0	1	1	0	0	0	0	0	0	2	0	0	1
ADO	GG genotype only	0	1	0	0	1	2	0	0	0	0	0	0	0	0
Correct genotype		5	4	4	4	3	3	5	5	3	4	2	3	5	4
Total		5	5	5	5	5	5	5	5	5	5	5	5	5	5
Mean of genotyping error rate (%)		10%		20%		40%		0%		30%		50%		10%

Allele-specific PCR was done with 5 replicates in two independent experiments
^aAllele-specific PCR was done using annealing temperatue of 54.3 °C
^bAllele-specific PCR was done using mixed DNA template of 1 ng AA genotype and 1 ng GG genotype