Detecting imbalanced expression of SNP alleles by minisequencing on microarrays

BMC Biotechnology

Table 2 Results for the regression lines describing the accuracy and limit of detection for the methods when analysing mixed samples of a dilution series.

SNP^a	Method^b	R^2c	Detection sensitivity (%)^d p < 0.05	p-value^e
rs4331 ACE	I	0.95	7.5	0.0076
	II	0.97	4.9	0.0107
rs1042713 ADRB2	I	0.99	4.9	0.00051
	II	0.98	2.1	0.000077
rs1042714 ADRB2	I	0.96	14 *	0.042
	II	0.98	8.9 *	0.047
rs1042718 ADRB2	I	0.99	14 *	0.020
	II	0.99	5.8 *	0.0011
rs1042719 ADRB2	I	0.90	5.8	0.0072
	II	0.96	1.0	0.013
rs1799983 NOS3	I	0.99	8.9 *	0.0015
	II	0.97	3.8 *	0.023
rs5351 EDNRB	I	0.87	5.8	0.016
	II	1.0	1.0	0.000016
rs5925 LDLR	I	1.0	4.9	0.014
	II	0.98	4.9	0.018
rs5930 LDLR	I	0.94	8.9	0.00030
	II	0.63	33	0.011
rs1433099 LDLR	I	0.75	ND	ND
	II	0.88	5.8	0.017

^a dbSNP ID number and gene name acronym.
^b Minisequencing using (I) immobilised primers; (II) cyclic primer extension and "tag-arrays".
^c Coefficient of determination describing the fit between the regression lines in Figure 1, and the data points.
^d Level at which the minority SNP allele can be detected. The percentages correspond to the mixture with a signal intensity ratio significantly different (p < 0.05) from the signal intensity ratio of the corresponding homozygous or heterozygous (*) sample. ND: Not possible to determine due to scatter of the data points.
^e p-value for difference between signal ratios at the detection level and at 0% of the minority allele.

ISSN: 1472-6750