Admixture Has Shaped Romani Genetic Diversity in Clinically Relevant Variants

Population history modulates the fitness effects of Copy Number Variation in the Roma

We provide the first whole genome Copy Number Variant (CNV) study addressing Roma, along with reference populations from South Asia, the Middle East and Europe. Using CNV calling software for short-read sequence data, we identified 3171 deletions and 489 duplications. Taking into account the known population history of the Roma, as inferred from whole genome nucleotide variation, we could discern how this history has shaped CNV variation. As expected, patterns of deletion variation, but not duplication, in the Roma followed those obtained from single nucleotide polymorphisms (SNPs). Reduced effective population size resulting in slightly relaxed natural selection may explain our observation of an increase in intronic (but not exonic) deletions within Loss of Function (LoF)-intolerant genes. Over-representation analysis for LoF-intolerant gene sets hosting intronic deletions highlights a substantial accumulation of shared biological processes in Roma, intriguingly related to signaling, nervous system and development features, which may be related to the known profile of private disease in the population. Finally, we show the link between deletions and known trait-related SNPs reported in the genome-wide association study (GWAS) catalog, which exhibited even frequency distributions among the studied populations. This suggests that, in general human populations, the strong association between deletions and SNPs associated to biomedical conditions and traits could be widespread across continental populations, reflecting a common background of potentially disease/trait-related CNVs.

Genetic Determinants of Leisure-Time Physical Activity in the Hungarian General and Roma Populations

Leisure-time physical activity (LTPA) is one of the modifiable lifestyle factors that play an important role in the prevention of non-communicable (especially cardiovascular) diseases. Certain genetic factors predisposing to LTPA have been previously described, but their effects and applicability on different ethnicities are unknown. Our present study aims to investigate the genetic background of LTPA using seven single nucleotide polymorphisms (SNPs) in a sample of 330 individuals from the Hungarian general (HG) and 314 from the Roma population. The LTPA in general and three intensity categories of it (vigorous, moderate, and walking) were examined as binary outcome variables. Allele frequencies were determined, individual correlations of SNPs to LTPA, in general, were determined, and an optimized polygenetic score (oPGS) was created. Our results showed that the allele frequencies of four SNPs differed significantly between the two study groups. The C allele of rs10887741 showed a significant positive correlation with LTPA in general (OR = 1.48, 95% CI: 1.12-1.97; p = 0.006). Three SNPs (rs10887741, rs6022999, and rs7023003) were identified by the process of PGS optimization, whose cumulative effect shows a strong significant positive association with LTPA in general (OR = 1.40, 95% CI: 1.16-1.70; p < 0.001). The oPGS showed a significantly lower value in the Roma population compared with the HG population (oPGS_Roma: 2.19 ± SD: 0.99 vs. oPGS_HG: 2.70 ± SD: 1.06; p < 0.001). In conclusion, the coexistence of genetic factors that encourage leisure-time physical activity shows a more unfavorable picture among Roma, which may indirectly contribute to their poor health status.

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

The CYP2D6 gene encodes an enzyme responsible for the metabolism of ~20% of clinically prescribed drugs. In this study, 18 SNPs from the enhancer and promoter regions of CYP2D6 in 323 Roma from Croatia were genotyped, to find out whether the demographic history of Roma affected the distribution of the studied SNPs and their linkage disequilibrium (LD) values, with the major SNPs defining the CYP2D6 star alleles. No differences were found between the three Roma groups in allele and genotype frequencies. The distribution of LD values of Roma was compared with LD values of European and Asian populations. Regulatory CYP2D6 SNPs (rs5758550, rs28624811, rs1080985 and rs1080983) showed similar distribution and the highest LDs with rs16947 from the gene-coding region in all populations. In the promoter region, a complete LD between rs1080989 and rs28588594, and between rs1080983 and rs28624811, was found in Croatian Roma and investigated populations from 1000 genomes. A high LD was also found between rs1080985 from the promoter and rs5758550 from the enhancer region. SNP rs28735595 from the gene promoter region had the highest LD, with two gene region SNPs, rs1058164 and rs1135840. To conclude, the Croatian Roma population shows an LD pattern of the CYP2D6 gene region similar to the 1000 Genomes European and Asian populations.

Low prevalence of spectacle use in the Hungarian Roma population indicates unmet health needs

The Roma population is the largest transnational ethnic minority group in Europe, often facing socioeconomic inequalities and various health problems. In the present study, we investigated visual acuity and its influencing factors along with spectacle use of the Roma population in comparison with the general population in Hungary. A cross-sectional survey was carried out including 832 participants aged 20–64 years. We recorded the uncorrected visual acuity along with anthropometric, demographic, socioeconomic and health-related data of each individual. Although the average uncorrected visual acuity was somewhat higher, the use of a visual aid was significantly less frequent in the Roma population, especially in the group with a visual acuity below 0.5 in both eyes (14.3% vs. 77.1%, p < 0.001). Age, abdominal obesity and disturbances of carbohydrate metabolism had a negative impact on visual acuity in both populations; however, the latter was a much stronger risk factor in the Roma population (OR 5.789, 95% CI 2.239–14.964, p < 0.001) than in the general population (OR 2.075, 95% CI 1.097–3.926, p = 0.025). Our results show serious unmet health needs within the Roma population, which calls for public health programs to improve poor primary care indicators on regular eye examination and much more rigorous diabetes control.

Identification of recurrent pathogenic alleles using exome sequencing data: Proof-of-concept study of Russian subjects

Whole exome sequencing (WES) is a powerful tool for the cataloguing of population-specific genetic diseases. Within this proof-of-concept study we evaluated whether analysis of a small number of individual exomes is capable of identifying recurrent pathogenic alleles. We considered 106 exomes of subjects of Russian origin and revealed 13 genetic variants, which occurred more than twice and fulfilled the criteria for pathogenicity. All these alleles turned out to be indeed recurrent, as revealed by the analysis of 1045 healthy Russian donors. Eight of these variants (NAGA c.973G > A, ACADM c.985 A  >  C, MPO c.2031-2 A > C, SLC3A1 c.1400 T  >  C, LRP2 c.6160G > A, BCHE c.293 A  >  G, MPO c.752 T  >  C, FCN3 c.349delC) are non-Russian-specific, as their high prevalence was previously demonstrated in other European populations. The remaining five disease-associated alleles appear to be characteristic for subjects of Russian origin and include CLCN1 c.2680C  >  T (myotonia congenita), DHCR7 c.453G > A (Smith-Lemli-Opitz syndrome), NUP93 c.1162C  >  T (steroid-resistant nephrotic syndrome, type 12), SLC26A2 c.1957T  >  A (multiple epiphyseal dysplasia) and EIF3F c.694 T  >  G (mental retardation). These recessive disease conditions may be of particular relevance for the Russian Federation and other countries with significant Slavic population.