Table 3. Minisequencing results on the 3D-Link™-slides, the mercaptosilane-coated slides, the EZ-RAYS™-slides and the unmodified slides compared with those on the isothiocyanate-coated slides.

SNP		Signal intensitya (arbitrary fluorescence units)				Signal/noiseb
		3D-Link™	Isothiocyanate	Mercaptosilanec	Isothiocyanate	3D-Link™	Isothiocyanate	Mercaptosilanec	Isothiocyanate
AGTR1 1166co	C-allele	31 000	2500	21 000	8300	100	50	47	208
	A-allele	310	50	450	40
AGTR1 1166nc	G-allele	12 000	280	9300	10	24	7.0	47	0.013
	T-allele	500	40	200	780
AGTR1 1062co	A-allele	19 000	1400	21 000	7000	5.1	11	12	∞
	G-allele	3700	130	1800	0
AGTR1 1062nc	T-allele	27 000	3000	21 000	6900	250	300	46	53
	C-allele	110	10	460	130
eNOSco	G-allele	62 000	3500	60 000	24 000	370	88	38	4.8
	T-allele	170	40	1600	5000
eNOSnc	C-allele	7300	1200	17 000	3600	12	7.1	21	17
	A-allele	590	170	830	210
		EZ-RAYS™	Isothiocyanate	Unmodifiedd	Isothiocyanate	EZ-RAYS™	Isothiocyanate	Unmodifiedd	Isothiocyanate
eNOSco	G-allele	50	8500	6600	16 000	0.069	3.0	11	36
	T-allele	720	2800	610	440
eNOSnc	C-allele	4800	8400	16 000	4100	69	26	7.0	32
	A-allele	70	320	2300	130

^aSignal intensity = signal intensity of oligonucleotide spot – average background fluorescence. The average values were calculated from two different reactions using sample 1 as DNA template, which was homozygous at all SNP sites. The laser power was 85% for the 3D-Link™/isothiocyanate comparison and for the mercaptosilane/isothiocyanate comparison. For the other two comparison reactions the laser power was 95%. The pmt gain was 75% for the 3D-Link™/isothiocyanate comparison and 85% for all the other comparison reactions.

^bThe signal intensity ratio between the expected and the other possible allele.

^cThe AGTR1 1166 nc* oligonucleotide was used for the mercaptosilane-array whereas the isothiocyanate-array had the AGTR1 1166 co oligonucleotide (see Table 22).

^dThe oligonucleotide concentration was 15 µM for the unmodified oligonucleotides.