Clinical pharmacogenomics in action: design, assessment and implementation of a novel pharmacogenetic panel supporting drug selection for diseases of the central nervous system (CNS)

Table 1 Variant frequency associations and p-values

Gene variants	PGx–CNS-CEU	PGx–CNS-AFR	PGx–CNS-CHB
rs1799853	0.09 (0.08)	< 0.01 (0.23)	0.11 (0.09)
rs1057910	0.09 (0.08)	< 0.01 (0.22)	0.11 (0.09)
rs4244285	0.02 (0.11)	0.31 (0.06)	< 0.01 (0.22)
rs4986893	0.54 (0.03)*	0.60 (0.01)	< 0.01 (0.27)*
rs1051740	0.46 (0.05)	< 0.01 (0.27)	0.01 (0.13)
rs1065852	0.01 (0.11)	< 0.01 (0.14)	< 0.01 (0.35)
rs12248560	0.01 (0.11)	0.03 (0.10)	< 0.01 (0.26)
rs1414334	0.30 (0.06)	< 0.01 (0.48)	0.01 (0.15)
rs17782313	0.06 (0.09)	0.12 (0.08)	0.39 (0.06)
rs1799978	0.55 (0.08)*	< 0.01 (0.15)	< 0.01 (0.17)
rs1800497	0.22 (0.07)	< 0.01 (0.36)	< 0.01 (0.32)
rs2234922	0.74 (0.03)	< 0.01 (0.27)	< 0.01 (0.14)
rs2832407	0.03 (0.10)	< 0.01 (0.73)	< 0.01 (0.25)
rs28371725	0.35 (0.06)	< 0.01 (0.22)	0.01 (0.13)
rs28399504	0.12 (0.04)*	0.69 (0.05)*	> 0.99 (0.04)*
rs35742686	0.17 (0.08)*	0.03 (0.09)*	0.13 (0.08)*
rs3812718	0.41 (0.05)	< 0.01 (0.28)	0.75 (0.03)
rs3892097	0.40 (0.05)	< 0.01 (0.18)	< 0.01 (0.24)
rs4713916	0.34 (0.06)	< 0.01 (0.33)	0.08 (0.09)
rs489693	0.01 (0.13)	< 0.01 (0.32)	< 0.01 (0.14)
rs5030655	0.59 (0.01)*	0.59 (0.01)*	0.44 (0.04)
rs5030656	0.36 (0.03)*	0.59 (0.01)*	0.44 (0.04)*
rs7668258	0.43 (0.05)	< 0.01 (0.31)	< 0.01 (0.14)*
rs963468	0.75 (0.03)	< 0.01 (0.49)	0.60 (0.04)

Statistical results of the Chi-square pairwise comparisons of gene variant frequencies between the sample of this study (PGx–CNS, SEC) and the following populations: European CEU (commonly CEU: Northern and Western European ancestry); African, AFR (commonly YRI: Yoruba in Ibadan, Nigeria) and East Asian, CHB (commonly CHB: Han Chinese in Beijing, China). The presented output for each test includes its p-value and the corresponding Cramer’s V coefficient (in parenthesis). The comparisons for which the Fisher’s exact test of independence was additionally used (see “Materials and methods”) are indicated with an asterisk. The p-values in bold are those that remained significant (p-value < 0.01) after adjustment using the Holm-Bonferroni procedure. The degrees of freedom for all tests were two. Results show a very high correlation of variant frequencies in PGx–CNS and European CEU population, as compared to African and Chinese populations.

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