Several Different Lactase Persistence Associated Alleles and High Diversity of the Lactase Gene in the Admixed Brazilian Population

<div><p>Adult-type hypolactasia is a common phenotype caused by the lactase enzyme deficiency. The −13910 C>T polymorphism, located 14 Kb upstream of the lactase gene (<em>LCT</em>) in the <em>MCM6</em> gene was associated with lactase persistence (LP) in Europeans. This polymorphism is rare in Africa but several other variants associated with lactase persistence were observed in Africans. The aims of this study were to identify polymorphisms in the <em>MCM6</em> region associated with the lactase persistence phenotype and to determine the distribution of <em>LCT</em> gene haplotypes in 981 individuals from North, Northeast and South Brazil. These polymorphisms were genotyped by PCR based methods and sequencing. The −13779*C,−13910*T, −13937*A, −14010*C, −14011*T LP alleles previously described in the <em>MCM6</em> gene region that acts as an enhancer for the <em>LCT</em> gene were identified in Brazilians. The most common LP allele was −13910*T. Its frequency was highly correlated with European ancestry in the Brazilian populations investigated. The −13910*T was higher (0.295) in southern Brazilians of European ancestry and lower (0.175) in the Northern admixed population. <em>LCT</em> haplotypes were derived from the 10 <em>LCT</em> SNPs genotyped. Overall twenty six haplotypes previously described were identified in the four Brazilian populations studied. The Multidimensional Scaling analysis showed that Belém, in the north, was closer to Amerindians. Northeastern and southern Afro-descendants were more related with Bantu-speaking South Africans whereas the Southern population with European ancestry grouped with Southern and Northern Europeans. This study shows a high variability considering the number of <em>LCT</em> haplotypes observed. Due to the highly admixed nature of the Brazilian populations, the diagnosis of hypolactasia in Brazil, based only in the investigation of the −13910*T allele is an oversimplification.</p> </div

<i>LCT</i> haplotypes frequencies ± standard error in the Brazilian population.

<p>If only one chromosome was identified, the standard error was not estimated.</p>a<p>Nomenclature according to Hollox et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046520#pone.0046520-Hollox1" target="_blank">[14]</a>.</p>b<p>n = number of individuals.</p

F_ST values of haplotype frequencies among Brazilians and with the parental populations (Amerindians, Bantu-speaking population from Africa, Southern and Northern Europeans).

<p>F_ST values in bold are statistically significant (p<0.0001).</p>a<p>Haplotype frequencies from Friedrich et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046520#pone.0046520-Friedrich1" target="_blank">[26]</a>.</p>b<p>Haplotype frequencies from Hollox et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046520#pone.0046520-Hollox1" target="_blank">[14]</a>.</p

Number of −13779*C, −13937*A, −14010*C, and −14011*T alleles according to the population.

a<p>Heterozygous A and U <i>LCT</i> haplotypes.</p>b<p>Heterozygous A and P <i>LCT</i> haplotypes.</p>c<p>Homozygous A <i>LCT</i> haplotype.</p>d<p>Heterozygous C and U <i>LCT</i> haplotypes; heterozygous C and B <i>LCT</i> haplotypes.</p>e<p>Heterozygous A and g <i>LCT</i> haplotypes.</p>f<p>Homozygous A <i>LCT</i> haplotype; heterozygous A and E <i>LCT</i> haplotypes; heterozygous A and S <i>LCT</i> haplotypes.</p

Geographic location of the 3 Brazilian cities where the samples were collected.

<p>Geographic location of the 3 Brazilian cities where the samples were collected.</p

MDS of several populations <i>LCT</i> haplotypes.

<p>Nonmetric Multidimensional Scaling analysis of <i>LCT</i> haplotypes based on D_A distance showing the relationships among the four Brazilian populations with their parental groups: Brazilian Amerindians <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046520#pone.0046520-Friedrich1" target="_blank">[26]</a>; Southern Europeans, Northern Europeans, and Bantu-speaking South Africans <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046520#pone.0046520-Hollox1" target="_blank">[14]</a>. NorEur  =  Northern European, SouEur  =  Southern European, Euro  =  Porto Alegre Euro-descendant, Afro  =  Porto Alegre Afro-descendant.</p

Frequencies of the combinations found between the −13910 C>T and −22018 G>A alleles in the Brazilian population.

<p>Frequencies of the combinations found between the −13910 C>T and −22018 G>A alleles in the Brazilian population.</p

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

<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

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