A microarray-based system for the simultaneous analysis of single nucleotide polymorphisms in human genes involved in the metabolism of anti-malarial drugs

Hodel, Eva Maria; Ley, Serej D; Qi, Weihong; Ariey, Frédéric; Genton, Blaise; Beck, Hans-Peter

doi:10.1186/1475-2875-8-285

Table 4 Comparison of SNP data acquired either by sequencing or DNA microarray technology.

From: A microarray-based system for the simultaneous analysis of single nucleotide polymorphisms in human genes involved in the metabolism of anti-malarial drugs

		1^st wash			2^nd wash
SNP	Country	κ	n	%	κ	n	%	Agreement
CYP2A6*2	Cambodia	0.87	24	88.9	0.92	19	70.4	Substantial to almost
	Tanzania	0.83	58	82.9	0.61	53	75.7	perfect
CYP2B65*	Cambodia	0.94	27	100.0	0.94	27	100.0	Almost perfect
	Tanzania	0.92	67	95.7	0.86	67	95.7
CYP2B66*	Cambodia	0.42	26	96.3	0.42	27	100.0	Fair to moderate
	Tanzania	0.35	63	90.0	0.40	59	84.3
CYP2C83*	Cambodia	0.97	20	74.1	1.00	20	74.1	Substantial to almost
	Tanzania	0.90	39	55.7	0.79	38	54.3	perfect
CYP2C93*	Cambodia	0.92	26	96.3	0.94	26	96.3	Almost perfect
	Tanzania	0.90	67	95.7	0.82	64	91.4
CYP2C95*	Cambodia	0.98	27	100.0	1.00	27	100.0	Almost perfect
	Tanzania	0.93	67	95.7	0.86	70	100.0
CYP2C193*	Cambodia	1.00	27	100.0	1.00	26	96.3	Almost perfect
	Tanzania	0.90	97	95.7	0.83	66	94.3
CYP2D64*	Cambodia	0.98	26	96.3	1.00	26	96.3	Almost perfect
	Tanzania	0.91	63	90.0	0.88	65	92.9
CYP2D610* (100C>T)	Cambodia	0.59	24	88.9	0.64	20	74.1	Moderate to substantial
	Tanzania	0.72	31	44.3	0.76	27	38.6
CYP2D610* (4180G>C)	Cambodia	0,40	21	77.8	0.50	17	63.0	Fair to moderate
	Tanzania	0.45	45	64.3	0.51	38	54.3
CYP2D617* (1023C>T)	Cambodia	0.86	19	70.4	1.00	6	22.2	Moderate to almost
	Tanzania	0.59	37	52.9	0.49	37	52.9	perfect
CYP2D617* (2850C>T)	Cambodia	0.29	7	25.9	0.20	6	22.2	Slight to substantial
	Tanzania	0.66	20	28.6	0.59	21	30.0
CYP3A41B*	Cambodia	0.00	6	22.2	0.00	5	18.5	Slight to substantial
	Tanzania	0.76	23	32.9	0.69	22	31.4
CYP3A53*	Cambodia	0.39	21	77.8	0.42	17	63	Fair to substantial
	Tanzania	0.73	61	87.1	0.65	58	82.9
NAT25*	Cambodia	0.32	14	51.9	0.38	8	29.6	Fair to moderate
	Tanzania	0.47	37	52.9	0.53	28	40.0
NAT26*	Cambodia	0.70	26	96.3	0.73	25	92.6	Substantial
	Tanzania	0.74	62	88.6	0.71	62	88.6
NAT27*	Cambodia	0.72	25	92.6	0.70	22	81.5	Substantial
	Tanzania	0.75	55	78.6	0.67	49	70.0
NAT214*	Cambodia	1.00	27	100.0	1.00	27	100.0	Substantial to almost
	Tanzania	0.76	62	88.6	0.74	61	87.1	perfect

Data was acquired in 27 Cambodian and 70 Tanzanian malaria patients. κ indicates the kappa index. n is the number and % the percentage of samples with results for both techniques.

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ISSN: 1475-2875

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