Sequence polymorphism can produce serious artefacts in real-time PCR assays: hard lessons from Pacific oysters

Taris, Nicolas; Lang, Robert P; Camara, Mark D

doi:10.1186/1471-2164-9-234

BMC Genomics

Table 2 Ct values across families and primer pairs, obtained from the ABI 7500 real-time PCR instrument

From: Sequence polymorphism can produce serious artefacts in real-time PCR assays: hard lessons from Pacific oysters

a [GenBank:EX956386]
	Model effect		Family classification test (Tukey)
				Family
Primer pair		Pr > F	Pattern	4	25	34	65	Pattern
1	Family	0.02	Ct mean	28.03	28.24	28.25	27.67
	Replicate	0.68	SD	0.07	0.11	0.07	0.03
			Statistical grouping	ab	b	b	a	A
2	Family	< 0.01	Ct mean	33.72	36.49	35.29	29.82
	Replicate	0.42	SD	0.10	0.60	0.74	0.07
			Statistical grouping	b	b	b	a	A
3	Family	0.01	Ct mean	28.90	28.90	29.01	28.29
	Replicate	0.24	SD	0.10	0.15	0.03	0.06
			Statistical grouping	b	b	b	a	A
6	Family	< 0.01	Ct mean	31.26	31.84	31.51	30.51
	Replicate	0.26	SD	0.18	0.36	0.66	0.75
			Statistical grouping	b	b	a	ab	B
10	Family	< 0.01	Ct mean	41.47	42.18	43.43	35.93
	Replicate	0.42	SD	0.57	0.57	0.37	0.15
			Statistical grouping	b	b	b	a	A
11	Family	< 0.01	Ct mean	35.79	37.56	37.14	30.56
	Replicate	0.33	SD	0.38	0.38	0.95	0.49
			Statistical grouping	b	b	b	a	A
The statistical grouping refers to figures 2, 3 and 4, and corresponds to the result of a Tukey test based on level of cDNA expression and not Ct values.
b [GenBank:AJ565694]
3	Family	< 0.01	Ct mean	23.50	33.10	19.87	31.11
	Replicate	0.42	SD	0.16	0.19	0.12	0.21
			Statistical grouping	b	b	a	b	A
5	Family	< 0.01	Ct mean	23.85	33.71	19.68	30.30
	Replicate	0.39	SD	0.06	0.38	0.37	0.28
			Statistical grouping	b	b	a	b	A
6	Family	< 0.001	Ct mean	22.38	31.91	29.36	37.88
	Replicate	0.39	SD	0.12	0.09	0.08	0.29
			Statistical grouping	a	b	b	b	B
7	Family	0.01	Ct mean	22.27	31.77	19.34	29.43
	Replicate	0.41	SD	0.06	0.40	0.41	0.38
			Statistical grouping	b	b	a	b	A
8	Family	< 0.001	Ct mean	21.68	31.10	33.15	36.81
	Replicate	0.42	SD	0.08	0.09	0.56	0.61
			Statistical grouping	a	b	b	b	B
9	Family	< 0.01	Ct mean	23.90	34.44	20.34	32.16
	Replicate	0.44	SD	0.38	0.02	0.04	0.11
			Statistical grouping	b	b	a	b	A
12	Family	< 0.001	Ct mean	22.59	32.08	19.15	29.92
	Replicate	0.42	SD	0.02	0.09	0.02	0.18
			Statistical grouping	b	b	a	b	A
13	Family	< 0.01	Ct mean	21.05	30.56	25.11	35.64
	Replicate	0.40	SD	0.12	0.20	0.02	0.46
			Statistical grouping	a	b	b	b	B
14	Family	< 0.01	Ct mean	21.45	31.96	21.72	32.22
	Replicate	0.17	SD	0.67	0.28	0.02	0.26
			Statistical grouping	a	b	a	b	C

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ISSN: 1471-2164

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