Abstract
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 (LCT) in the MCM6 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 MCM6 region associated with the lactase persistence phenotype and to determine the distribution of LCT 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 MCM6 gene region that acts as an enhancer for the LCT 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. LCT haplotypes were derived from the 10 LCT 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 LCT 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.
Highlights
Adult-type hypolactasia or lactose intolerance (OMIM #223100) is a worldwide common phenotype determined by lactase deficiency, it is due to lactase activity decline after weaning
Identification of single nucleotide polymorphisms (SNPs) in the lactase gene (LCT) Enhancer Region The overall 213910*T allele frequency varied from 17.5% in the Northern admixed population to 29.5% in Southern Brazilians of European ancestry (Table 1)
Comparisons of the 213910*T allele frequencies of the four Brazilian populations with frequencies available in dsSNP-NCBI database showed that overall these frequencies differ from those described, some similarities could be observed
Summary
Adult-type hypolactasia or lactose intolerance (OMIM #223100) is a worldwide common phenotype determined by lactase deficiency, it is due to lactase activity decline after weaning. The lactase enzyme activity is to hydrolyze lactose, the main carbohydrate in milk [1]. A T/C polymorphism at position 213910 and an A/G polymorphism at position 222018 from the start codon of the LCT gene have been identified. These nucleotide variants are located in introns 9 and 13 of the neighboring MCM6 gene, the 213910*C allele associates 100% and the 222018*G allele associates approximately 97% with the lactase nonpersistent phenotype [6,7,8]. The derived allele 213910T increases promoter activity [8,9,10,11]
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