Untangling SNP Variations within CYP2D6 Gene in Croatian Roma

Abstract

CYP2D6 is a highly polymorphic gene whose variations affect its enzyme activity. To assess whether the specific population history of Roma, characterized by constant migrations and endogamy, influenced the distribution of alleles and thus phenotypes, the CYP2D6 gene was sequenced using NGS (Next Generation Sequencing) method - targeted sequencing in three groups of Croatian Roma (N = 323) and results were compared to European and Asian populations. Identified single nucleotide polymorphisms (SNPs) were used to reconstruct haplotypes, which were translated into the star-allele nomenclature and later into phenotypes. A total of 43 polymorphic SNPs were identified. The three Roma groups differed significantly in the frequency of alleles of polymorphisms 6769 A > G, 6089 G > A, and 5264 A > G (p < 0.01), as well as in the prevalence of the five most represented star alleles: *1, *2, *4, *10, and *41 (p < 0.0001). Croatian Roma differ from the European and Asian populations in the accumulation of globally rare SNPs (6089 G > A, 4589 C > T, 4622 G > C, 7490 T > C). Our results also show that demographic history influences SNP variations in the Roma population. The three socio-culturally different Roma groups studied differ significantly in the distribution of star alleles, which confirms the importance of a separate study of different Roma groups.

From Croatian Roma to 1000 Genomes: The Story of the CYP2D6 Gene Promoter and Enhancer SNPs

“…The non-function CYP2D6*4 allele, which is predominantly found in European populations (18%), had the highest frequency in the Balkan and Baranja Roma groups, even higher than in European populations. The prevalence of the allele *4 in the Medjimurje Roma group is lower than in the European population, but still higher than in other world populations [ 24 , 48 , 49 ]. Since both these star alleles have an impaired function, an additional analysis such as the reporter gene assay could help to untangle the effect of these promoter SNPs on CYP2D6 functionality.…”

“…The pharmacogenomics of the Roma minority population has been studied for the last few years [ 33 ]. These studies included SNPs in several ADME genes, such as ABCB1 [ 34 , 35 ], CYP2B6 [ 36 , 37 , 38 ], CYP2C19 [ 39 , 40 , 41 , 42 ], CYP2D6 [ 24 , 37 , 38 , 41 ] and NAT [ 42 , 43 ].…”

“…Previous analyses showed that the three socio-culturally different Croatian Roma groups show significant differences in allele distribution within the CYP2D6 gene [ 24 ], and therefore we continued to investigate promoter and enhancer SNPs associated with this gene. In general, diversity in regulatory elements has an impact on gene expression, so understanding it could help to elucidate the unexplained variability in gene activity [ 11 ].…”

“…CYP2D6*10 is a decreased-function allele predominantly found in East and South Asian populations, where its prevalence ranges from 9% to 44%. Its frequency in African populations is between 4% and 6%, among Europeans, <2%, and in the Croatian Roma, 6% [ 24 , 48 , 49 ]. The non-function CYP2D6*4 allele, which is predominantly found in European populations (18%), had the highest frequency in the Balkan and Baranja Roma groups, even higher than in European populations.…”

“…The KASP genotyping assay is a form of competitive allele-specific PCR combined with a homogeneous fluorescent SNP genotyping system, which determines the alleles at a specific locus within genomic DNA [ 23 ]. Data for the CYP2D6 star allele-defining SNPs (rs1135840, rs16947, rs28371725, rs3892097, rs1058164, rs1065852 and rs769258) in Croatian Roma were taken from a paper by Stojanović Marković et al [ 24 ].…”