Comparison of variation in frequency for SNPs associated with asthma or liver disease between Estonia, HapMap populations and the 1000 genome project populations

Abstract

Allele‐specific analyses to understand frequency differences across populations, particularly populations not well studied, are important to help identify variants that may have a functional effect on disease mechanisms and phenotypic predisposition, facilitating new Genome‐Wide Association Studies (GWAS). We aimed to compare the allele frequency of 11 asthma‐associated and 16 liver disease‐associated single nucleotide polymorphisms (SNPs) between the Estonian, HapMap and 1000 genome project populations. When comparing EGCUT with HapMap populations, the largest difference in allele frequencies was observed with the Maasai population in Kinyawa, Kenya, with 12 SNP variants reporting statistical significance. Similarly, when comparing EGCUT with 1000 genomes project populations, the largest difference in allele frequencies was observed with pooled African populations with 22 SNP variants reporting statistical significance. For 11 asthma‐associated and 16 liver disease‐associated SNPs, Estonians are genetically similar to other European populations but significantly different from African populations. Understanding differences in genetic architecture between ethnic populations is important to facilitate new GWAS targeted at underserved ethnic groups to enable novel genetic findings to aid the development of new therapies to reduce morbidity and mortality.

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“…1B). The '1000 Genomes Project' phase 3 has systematically completed mapping the genomes of >2,500 individuals for genetic variation (32) of the five major groups, including Europeans, Africans, Americans, East Asians and South Asians (33,34).…”

“…of the human population. The incidence of different genetic variants in a population, represented by their allele frequency, is a reflection of the genetic diversity, and changes in allele frequencies over time can indicate that genetic drift is occurring or that new significant variants have been introduced into the population (34)(35)(36)(37). From the '1000 Genomes Project' database (32), each identified variant is described by a specific allele frequency, which is estimated by dividing the number of times the allele of interest is observed in the population by the total number of incidence of all the alleles present for that particular genetic locus in the population (38,39).…”

“…From the '1000 Genomes Project' database (32), each identified variant is described by a specific allele frequency, which is estimated by dividing the number of times the allele of interest is observed in the population by the total number of incidence of all the alleles present for that particular genetic locus in the population (38,39). The '1000 Genomes Project' provides the general allele frequency of the identified variants and the corresponding allele frequencies of the five major groups, including Europeans, Africans, Americans, East Asians and South Asians (33,34). Allele frequencies are presented as a decimal in the range of 0-1.…”