Screening of variants for lactase persistence/non-persistence in populations from South Africa and Ghana

Abstract

Background: Lactase non-persistence is a condition where lactase activity is decreased in the intestinal wall after weaning. In European derived populations a single nucleotide polymorphism (SNP) C/T -13910 residing 13.9 kb upstream from the lactase gene has been shown to define lactase activity, and several other single nucleotide polymorphisms

Diagnosis of adult-type hypolactasia/lactase persistence: genotyping of single nucleotide polymorphism (SNP C/T-13910) is not consistent with breath test in Colombian Caribbean population

“…Thus, the low frequency of the -13910T allele found in the present study most likely represents the European contribution to the mixture of the three main ethnicities of the Colombian Caribbean people, whereas the high frequency of -13910C allele would represent the contribution from the other two ethnicities (Amerindians and Africans) (17) . The above hypothesis agrees with the Torniainen et al (29) and Mattar et al (16) studies. The former found in South Africa and Ghana that both -13910*T and -14010*C alleles reflected the contribution from Europeans and Africans in mixed ancestry subjects, respectively; the latter study reported that the lactase persistence allele (-13910*T) in mestizos subjects, product of white and African-Brazilian interbreeding, is present not only as a consequence of the European contribution but also of the ancestral contribution of Africans who have that allele (9,16,28) .…”

“…The former found in South Africa and Ghana that both -13910*T and -14010*C alleles reflected the contribution from Europeans and Africans in mixed ancestry subjects, respectively; the latter study reported that the lactase persistence allele (-13910*T) in mestizos subjects, product of white and African-Brazilian interbreeding, is present not only as a consequence of the European contribution but also of the ancestral contribution of Africans who have that allele (9,16,28) . This is not the case for African Caribbean Colombians, because the blacks brought as slaves from Africa during the colonial period came mainly from Western Africa where the -13910*T allele is scarce (18,29) . The importance of the ethnic origin, when doing genotype-phenotype correlation studies is evident with the results recently published in Brazil by Bulhões et al (3) and Mattar et al (15) who reported perfect correlation between the SNP C/T -13910 and lactose digestion.…”

Functional Significance of Single Nucleotide Polymorphisms in the Lactase Gene in Diverse US Patients and Evidence for a Novel Lactase Persistence Allele at −13909 in Those of European Ancestry

“…Another 38 SNPs were chosen to determine the continental ancestry of individuals in the panel (25). Three African-derived lactase SNPs (-14010G/C, -13915T/G, and -13907C/G) were genotyped as well (11, 26). In order to be included for analysis, SNPs were required to pass quality control measures, including genotyping greater than 90 percent in the sample, and being in Hardy-Weinberg equilibrium.…”

The −14010*C variant associated with lactase persistence is located between an Oct-1 and HNF1α binding site and increases lactase promoter activity

“…A -14010*C variant is associated with LP in Kenya and Tanzania (Tishkoff et al 2007). This variant has recently also been found to be relatively frequent in Xhosa population in South Africa and in Ghana (Torniainen et al 2009). Several other rare SNPs which are likely to be associated with LP have recently also been reported (Ingram et al 2007(Ingram et al , 2009aKhabarova et al 2010;Lember et al 2006;Tag et al 2007).…”