Distribution of <i>CYP2D6</i> Alleles and Phenotypes in the Brazilian Population

<div><p>Abstract</p><p>The CYP2D6 enzyme is one of the most important members of the cytochrome P450 superfamily. This enzyme metabolizes approximately 25% of currently prescribed medications. The <i>CYP2D6</i> gene presents a high allele heterogeneity that determines great inter-individual variation. The aim of this study was to evaluate the variability of <i>CYP2D6</i> alleles, genotypes and predicted phenotypes in Brazilians. Eleven single nucleotide polymorphisms and <i>CYP2D6</i> duplications/multiplications were genotyped by TaqMan assays in 1020 individuals from North, Northeast, South, and Southeast Brazil. Eighteen <i>CYP2D6</i> alleles were identified in the Brazilian population. The <i>CYP2D6*1</i> and <i>CYP2D6*2</i> alleles were the most frequent and widely distributed in different geographical regions of Brazil. The highest number of <i>CYPD6</i> alleles observed was six and the frequency of individuals with more than two copies ranged from 6.3% (in Southern Brazil) to 10.2% (Northern Brazil). The analysis of molecular variance showed that <i>CYP2D6</i> is homogeneously distributed across different Brazilian regions and most of the differences can be attributed to inter-individual differences. The most frequent predicted metabolic status was EM (83.5%). Overall 2.5% and 3.7% of Brazilians were PMs and UMs respectively. Genomic ancestry proportions differ only in the prevalence of intermediate metabolizers. The IM predicted phenotype is associated with a higher proportion of African ancestry and a lower proportion of European ancestry in Brazilians. PM and UM classes did not vary among regions and/or ancestry proportions therefore unique <i>CYP2D6</i> testing guidelines for Brazilians are possible and could potentially avoid ineffective or adverse events outcomes due to drug prescriptions.</p></div

Pairwise F_ST (95% Confidence Interval) among Brazilian regions and grouped according to color.

<p>Pairwise F_ST (95% Confidence Interval) among Brazilian regions and grouped according to color.</p

<i>CYP2D6</i> allele frequencies in Brazil.

a<p>SNP combination that could not be assigned to a known allele, for more information see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110691#pone.0110691.s003" target="_blank">Table S3</a>.</p><p>χ² = 70.184 and p-value = 0.069 for the comparison of the allele frequencies among the four regions.</p><p><i>CYP2D6</i> allele frequencies in Brazil.</p

<i>CYP2D6</i> genotyped polymorphisms, inferred alleles and estimated enzyme activity.

<p>Nucleotides in bold are the polymorphic sites.</p><p>Decr = decreased activity.</p><p>Incr = increased activity.</p><p>ND = activity not determined.</p>a<p>According to The Human Cytochrome P450 (CYP) Allele Nomenclature Database <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110691#pone.0110691-Antunes1" target="_blank">[33]</a>.</p>b<p>Deletion of the entire <i>CYP2D6</i> gene.</p><p>SNPs ID numbers are listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110691#pone.0110691.s002" target="_blank">Table S2</a>.</p><p><i>CYP2D6</i> genotyped polymorphisms, inferred alleles and estimated enzyme activity.</p

AMOVA results for the allele frequencies of the sample stratified by region and by self-reported skin color.

<p>*Four Brazilian regions were considered: North, Northeast, Southeast, and South.</p><p>**Three skin color categories were considered: Black, Brown and White.</p><p>AMOVA results for the allele frequencies of the sample stratified by region and by self-reported skin color.</p

Genetic ancestry (mean ± standard deviation) proportions according to CYP2D6 phenotypes.

a<p>P-value for the Kruskal-Wallis One-Way ANOVA.</p>b<p>Significantly higher mean in the pairwise comparisons. FDR adjusted p-values for the IM×PM, IM×EM, and IM×UM comparisons are, respectively: 0.0014, 0.011, and 0.048.</p>c<p>Significantly higher mean in the pairwise comparisons with EM and UM phenotypes. FDR adjusted p-values for the IM×EM, and IM×UM comparisons are, respectively: 0.018, 0.027.</p><p>Genetic ancestry (mean ± standard deviation) proportions according to CYP2D6 phenotypes.</p

CYP2D6 predicted phenotype frequencies according to self-reported color and geographical region.

a<p>Not Determined.</p><p>The Multinomial Log-Linear analysis: self-reported skin color is not associated with the predicted phenotype (p = 0.089); region is not associated with the predicted phenotype (p = 0.467).</p><p>CYP2D6 predicted phenotype frequencies according to self-reported color and geographical region.</p

Copy number variation of the <i>CYP2D6</i> in the Brazilian population.

<p>Copy number variation of the <i>CYP2D6</i> in the Brazilian population.</p

Relative percentage of the Col1.7G2 clone of <i>T. cruzi</i> in tissues of C57Blk6 (<i>H2^b</i>) and C57BlkSj (<i>H2^d</i>) after six months of double infection with Col1.7G2 and JG strains, using the LSSP-PCR technique.

<p>Each point indicates data from individual mice and the bar represents the median value.</p

Quantitative analyses of the percentage of Col1.7G2 and/or JG after intracellular development in distinct murine cardiac explants exposed to equal mixture of trypomastigote forms of each population.

<p>(a) Relative percentage of the Col1.7G2 clone using the LSSP-PCR technique, 24, 96 and 120 h post-infection in murine cardiac explants. P values above the bars were obtained by the two-sample Student t test and indicate significant differences between explants of congenic animals. One asterisk (*) indicates statistically significant differences between BALB/B10 (<i>H2^b</i>) and BALB/c (<i>H2^d</i>) and two asterisks (**) between C57BL/6 (<i>H2^b</i>) and C57BLKS/J (<i>H2^d</i>). (b) D7 allele melting curves obtained from the real time PCR of cardiac explants of murine mice. (NC) indicates the negative control melting curves obtained from different non-infected explant samples; (Std) indicates the melting curves obtained from the real time PCR of artificial mixtures of equal amounts of JG and Col1.7G2 DNA. In all other graphs, it is shown the melting curves obtained from explants of each different mouse strains infected with a mixture of Col1.7G2 and JG. For these graphs the red curves correspond to the amount of each <i>T. cruzi</i> population (Col1.7G2 and JG) obtained from the experimentally double infected cardiac explants, while the green curves are superimposed standard curves obtained from the real time PCR of the parasite artificial mixtures. The peaks corresponding to the specific D7 alleles for each <i>T. cruzi</i> DNA population (Col1.7G2 – 81.5°C and JG – 78.2°C), are indicated with a black line.</p