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

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

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

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

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

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

<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

Genotypic and allelic distribution of SNPs on <i>CYP2E1</i> and <i>GSTM1</i> genes among patients grouped according to clinical evolution.

*<p>¹p-value;</p>*<p>²OR-odds ratio, CI-confidence interval.</p

Combined and isolated genotypic distribution of <i>CYP2E1</i> gene (SNPs 1053T>C, 1293C>G and 7632T>A), and deletion (<i>GSTM1</i>^*<i>1/GSTM1</i>^*<i>0</i>) on gene <i>GSTM1</i> of patients classified accordingly to baciloscopic index BI (LBI and HBI).

*<p>¹p-value;</p>*<p>²OR-odds ratio, CI-confidence interval;</p>*<p>³Combined effect of mutant alleles of distinct genes.</p

Allele and genotype distributions of CYP2E1 and GSTM1 genes within two samples from leprosy patients and healthy individuals.

<p>Allele and genotype distributions of CYP2E1 and GSTM1 genes within two samples from leprosy patients and healthy individuals.</p