Quantify single nucleotide polymorphism (SNP) ratio in pooled DNA based on normalized fluorescence real-time PCR

BMC Genomics

Table 3 Summary of the fluorescence ratio based method and the Ct base method for quantification of predefined standards

Group No. In predefined standards	Predefined allele ratio YMDD:	K_f method			Baseline subtracted fluorescence ratio			SDM
	YIDD	Mean (n = 4)^a	S.D (n = 4)^b	Intra C.V^c	Mean (n = 4)^d	S.D (n = 4)^e	Intra C.V^c	Mean (n = 4)^f	S.D (n = 4)^g	Intra C.V^c
1	90%: 10%	2.68	0.32	11.80%	8.31	0.99	11.95%	6.46	3.06	47.29%
2	80%: 20%	1.40	0.08	5.45%	4.25	0.27	6.45%	2.73	0.09	3.30%
3	70%: 30%	0.80	0.14	17.22%	2.15	0.69	31.87%	1.46	0.14	9.32%
4	60%: 40%	0.54	0.03	6.11%	1.38	0.17	12.22%	1.09	0.27	24.43%
5	50%: 50%	0.40	0.03	7.30%	1.12	0.17	15.59%	0.65	0.07	10.38%
6	40%: 60%	0.30	0.02	7.77%	0.76	0.10	13.09%	0.51	0.04	8.56%
7	30%: 70%	0.22	0.00	1.91%	0.62	0.03	4.89%	0.32	0.08	25.12%
8	20%: 80%	0.15	0.01	3.67%	0.39	0.03	6.57%	0.43	0.18	42.29%
9	10%: 90%	0.07	0.01	10.24%	0.17	0.01	5.98%	0.01	0.02	113.30%
Av.	Average CV			7.94%			12.07%			31.56%

The spreadsheet used for this analysis is available as Supplementary Material.1 [see Additional file 1]
a. Arithmetic mean K_f of 4 replicates
b. Combined Standard deviation K_f for 4 replicates
c. (SD/mean) × 100%
d. Fluorescence ratio arithmetic mean of 4 replicates
e. Combined Standard deviation fluorescence ratio for 4 replicates
f. Arithmetic mean 2^-ΔCt of 4 replicates
g. Standard deviation of 2^-ΔCt for 4 replicates

ISSN: 1471-2164