Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways.

To newly identify loci for age at natural menopause, we carried out a meta-analysis of 22 genome-wide association studies (GWAS) in 38,968 women of European descent, with replication in up to 14,435 women. In addition to four known loci, we identified 13 loci newly associated with age at natural menopause (at P < 5 × 10(-8)). Candidate genes located at these newly associated loci include genes implicated in DNA repair (EXO1, HELQ, UIMC1, FAM175A, FANCI, TLK1, POLG and PRIM1) and immune function (IL11, NLRP11 and PRRC2A (also known as BAT2)). Gene-set enrichment pathway analyses using the full GWAS data set identified exoDNase, NF-κB signaling and mitochondrial dysfunction as biological processes related to timing of menopause.

The role of the Vlax Roma in shaping the European Romani maternal genetic history.

The Roma are comprised of many founder groups of common Indian origins but different socio-cultural characteristics. The Vlax Roma are one of the founder Roma populations characterized by a period of bondage in the historic Romanian principalities, and by the archaic Romanian language. Demographic history suggests different migration routes of Roma populations, especially after their arrival in Mesopotamia and the eastern boundary of the Byzantine Empire. Although various genetic studies of uniparental genetic markers showed a connection between Roma genetic legacy and their migration routes, precise sampling of Roma populations elucidates this relationship in more detail. In this study, we analyzed mitochondrial DNA of 384 Croatian Vlax Roma from two geographic locations in the context of 734 European Roma samples. Our results show that Roma migration routes are marked with two Near-Eastern haplogroups, X2 and U3, whose inverse proportional incidence clearly separates the Balkan and the Vlax Roma from other Roma populations that reached Europe as part of the first migration wave. Spatial and temporal characteristics of these haplogroups indicate a possibility of their admixture with Roma populations before arrival in Europe. Distribution of haplogroup M35 indicates that all Vlax Roma populations descend from one single founder population that might even reach back to the original ancestral Indian population. Founder effects followed by strict endogamy rules can be traced from India to contemporary small, local communities, as in the case of two Croatian Vlax Roma populations that show clear population differentiation despite similar origins and shared demographic history.

A quantitative trait locus for SBP maps near KCNB1 and PTGIS in a population isolate.

BACKGROUND: Population isolates are characterized by simplified genetic background and as such present promising opportunities for studying complex diseases. We performed a genome-wide linkage analysis for systolic (SBP) and diastolic blood pressure (DBP) followed up by the association analysis in the Croatian isolated island of Vis, where a very high prevalence of hypertension was reported (75%). METHODS: Variance-components linkage analysis was used to map quantitative trait loci (QTL) for SBP and DBP in 125 families with 1,389 members. Follow-up association analysis was performed in a sample of 421 subjects from the island of Vis. The 15 top-ranking single nucleotide polymorphisms (SNPs) were selected and tested for the association by in silico replication in the British 1958 Birth Cohort DNA Collection. RESULTS: Linkage results showed evidence for a QTL influencing DBP (lod = 1.89) on chromosome 7p14.2 and two QTL influencing SBP (lod = 2.03 on chromosome 1p36 and lod = 1.75 on chromosome 20q13). For the association results, the replication was observed for the rs237484 polymorphism on chromosome 20 that was associated with SBP with the effect size beta = -5.2 (P = 0.001; per A allele) in Vis population and beta = -1.1 (P = 0.04) in the British 1958 Birth Cohort. rs237484 is in proximity to the potassium voltage gate channel gene (KCNB1) and close to the prostaglandin I2 (prostacyclin) synthase gene (PTGIS). CONCLUSIONS: These results provide evidence of a QTL influencing blood pressure (BP) variability in this region and support the notion that the isolated population of the island of Vis is a suitable population for conducting linkage and association analyses of cardiovascular-related phenotypes.

Dissecting the molecular architecture and origin of Bayash Romani patrilineages: genetic influences from South-Asia and the Balkans.

The Bayash are a branch of Romanian speaking Roma living dispersedly in Central, Eastern, and Southeastern Europe. To better understand the molecular architecture and origin of the Croatian Bayash paternal gene pool, 151 Bayash Y chromosomes were analyzed for 16 SNPs and 17 STRs and compared with European Romani and non-Romani majority populations from Europe, Turkey, and South Asia. Two main layers of Bayash paternal gene pool were identified: ancestral (Indian) and recent (European). The reduced diversity and expansion signals of H1a patrilineages imply descent from closely related paternal ancestors who could have settled in the Indian subcontinent, possibly as early as between the eighth and tenth centuries AD. The recent layer of the Bayash paternal pool is dominated by a specific subset of E1b1b1a lineages that are not found in the Balkan majority populations. At least two private mutational events occurred in the Bayash during their migrations from the southern Balkans toward Romania. Additional admixture, evident in the low frequencies of typical European haplogroups, J2, R1a, I1, R1b1b2, G, and I2a, took place primarily during the early Bayash settlement in the Balkans and the Romani bondage in Romania. Our results indicate two phenomena in the Bayash and analyzed Roma: a significant preservation of ancestral H1a haplotypes as a result of considerable, but variable level of endogamy and isolation and differential distribution of less frequent, but typical European lineages due to different patterns of the early demographic history in Europe marked by differential admixture and genetic drift.

Y-STR genetic diversity of Croatian (Bayash) Roma.

Seventeen Y-chromosomal short tandem repeats (STRs) (DYS19, DYS385, DYS389I, DYS398II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATA H4.1) were typed in DNA samples from 146 unrelated adult Romani Bayash men from eastern and northwestern Croatia. Analysed Croatian Bayash Romani population represents an example of genetically homogenous population characterised by low levels of haplotype diversity and unique haplotype ratio as well as sharing of the same most frequent (founding) haplotype and its close derivatives by more than one third of the analyzed men. Despite almost exclusive sharing of the same minimal haplotype and its closely related derivates on the background of the Indian Y SNP haplogroup H1, we observed considerable level of genetic differentiation of Romani populations across Europe that should not be neglected in forensic statistics.

Traditional CVD risk factors and socio-economic deprivation in Roma minority population of Croatia.

Researches into health inequalities consistently show disadvantages in health status, morbidity and mortality for various ethnic minority groups. Current knowledge about prevention of cardiovascular diseases (CVD) mainly derives from studies carried out in populations of European origin while the evidences involving Roma population are scarce. Roma, an ethnic minority of northern Indian origin, live in many countries throughout the world and are well known for preserved traditions and resistance to assimilation. They are most often marginalized economically, spatially, politically and in terms of culture. In order to assess the health status and health-related lifestyle attributes, a multidisciplinary anthropological and epidemiological community-based study was carried out including a total of 423 members of the Bayash Roma minority population living in two regions of Croatia (144 men and 279 women, aged 18-84 yrs). Hypertension (HT) was found in 24.8% Bayash Roma (21.5% men and 26.5% women) using standard diagnostic criteria (i.e. BP > or = 140/90 mm Hg or taking antihypertensive therapy). The prevalence increases from 5.9% in the age group 18-34 yrs; 35.0% in the age group 35-64 yrs, and 51.4% in the age group 65+ yrs. The prevalence of hypertension in the Bayash Roma is almost half of the magnitude of what is usually reported for the general population of Croatia. It is also lower when compared with other European populations and this finding is not due to comparatively younger average age of the Bayash sample. The significant association of hypertension with age and BMI was confirmed in this study and the importance of non-traditional SES-related CVD risk factors was highlighted. Smoking is a part of traditional Roma life-style and with 70% of smokers almost the entire population is equally exposed to this risk factor in their family environment. Since homogenously distributed, this risk factor did not show to be a significant predictor of hypertension. The extent to which hypertension is influenced by traditional CVD risk factors as well as by some SES indicators was also assessed using a forward stepwise method of the multivariate logistic analysis. Each risk factor was explored as quantitative variable as well as qualitative one using various cut-offs. The best model showed to be the one having age and BMI presented as quantitative variables and sex, region, smoking status, income and schooling years as categorical ones; with cut-off 3 for number of income sources and 8 for the number of schooling years. In spite of the low prevalence of hypertension, the presented results are showing that Bayash Roma are bearing a high CVD risk factors load. We expect that with westernization of their life-style and along with increase of the economic power, the proportion of CVD in population of Bayash Roma will also increase. Therefore, it is important to recognize the need for early cardiovascular disease risk factors prevention in this minority population.

Effects of isolation and inbreeding on human quantitative traits: an example of biochemical markers of hemostasis and inflammation.

Isolation is a known force in evolutionary biology and one of the main factors in speciation. One of the main consequences of severe isolation is reduced mate choice, which results in the occurrence of inbreeding as a result of isolation. We investigated the effects of individual genome-wide heterozygosity measured as the multilocus heterozygosity (MLH) on biochemical markers of hemostasis and inflammation in 1,041 individuals from the island of Vis, Croatia, where inbreeding is prevalent and a wide range of variation in the genome-wide heterozygosity is expected. Assessment of individual genome-wide heterozygosity was based on genome-wide scans using 800 microsatellite (STR) and 317,503 single nucleotide (SNP) polymorphic markers in each examinee. In addition, for each examinee we defined a personal genetic history (PGH) based on genealogical records. The association between PGH and MLH and fibrinogen, D-dimer (Dd), von Willebrand factor (vWF), tissue plasminogen activator (tPA), and C-reactive protein (CRP) was performed with a mixed model, controlling for possible confounding effects. PGH was a significant predictor only for tPA (P < 0.001), whereas neither of the two MLH measures exhibited significant association with any of the investigated traits. The effects of individual genome-wide heterozygosity are most likely expressed in highly polygenically determined traits or in traits that are mediated by rare and recessive genetic variants. Weak associations between PGH and MLH and markers of hemostasis and inflammation suggest that their genetic control may not be highly polygenic and that they could be promising targets for genetic association studies.

Trapped between tradition and transition--anthropological and epidemiological cross-sectional study of Bayash Roma in Croatia.

AIM: To assess the key characteristics related to living conditions and health in the Bayash Roma population in Baranja and Medimurje regions of Croatia and identify possible demographic and socio-economic sources of variance in self-reported health and reproductive profile. METHODS: The study comprised a total of 266 adult Bayash individuals from Baranja and 164 from Medimurje (aged 41.3+/-15.1 years). Data on ethno-historical and demographic background, self-identity, life and hygiene conditions, education, employment, health insurance, and health (dietary and smoking habits, reproductive characteristics, diagnosed and undiagnosed health problems, use of medications). were obtained through interviews. Bivariate and multivariate methods were used in statistical analyses. RESULTS: The reported migratory pattern demonstrated that 88.8% of the examinees were born in the region of residence, which showed that the Bayash population was autochthonous and sedentary one. Financially, the Bayash primarily relayed on social welfare support allowance (84%) and child allowance (47%), while merely 2% were permanently and 23% occasionally employed. The proportion of the Bayash who had never attended school amounted to 33.3% (19.3% men and 40.6% women). The access to public water supply system was available to 52.5% of examinees, whereas only 1.7% had public sewage system, and 23.4% had private septic tanks. The most commonly reported health burden were frequent headaches (20.3%), stomach pain (16.3%), anxiety or insomnia (13.1%), hypertension (9.3%), and chronic obstructive pulmonary disease (COPD) (8.6%). The logistic regression identified level of education (odds ratio [OR], 0.77; 95% confidence interval [CI], 0.63-0.94) and access to health insurance (OR, 4.32; 95% CI, 1.46-12.77) as socio-economic/life-style factors playing a significant role in the occurrence of COPD. CONCLUSION: Our results indicate poor inclusion of the Bayash in the essential social service sectors such as health care, education, and employment, as well as substandard living conditions and unfavorable health-related behavior. Since education and health insurance were found to have significant effects on the observed reproductive status and self-reported health, they should be targeted in planning public health actions for socially marginalized and economically deprived groups.

An mtDNA perspective of French genetic variation.

BACKGROUND: The French has been insufficiently characterized so far for mitochondrial DNA (mtDNA) diversity. AIMS: The study aimed to enhance the information available for the French mtDNA pool and to explore the potential microgeographical differentiation of two French regions selected for their linguistic and historical idiosyncrasies. SUBJECTS AND METHODS: A total of 868 samples from 12 different locations in France were collected. They were sequenced for the hypervariable segment I (HVS-I) and typed for haplogroup defining markers from the coding region either by restriction fragment length polymorphism (RFLP) or by a new protocol based on the 5' nuclease allelic discrimination. The mtDNA gene pools of French Basques and Bretons were compared in terms of frequency and composition with relevant neighbouring populations. RESULTS: The French Basques' mtDNA pool shares some common features with that of the Spanish Basques, such as the high frequency of haplogroup H. However, the French Basques exhibit a number of distinct features, most notably expressed in the prevalence of haplogroups linked with the Neolithic diffusion in Europe. In Brittany, Finistère shows closer affinities with Britain and Scandinavia than the two other departments of Brittany. CONCLUSION: The mtDNA haplogroup composition of the French does not differ significantly from the surrounding European genetic landscape. At a finer grain, microgeographical differentiation can be revealed, as shown for the French Basque country and for Brittany.

Calcaneous ultrasonographic assessment of bone mineral density in the Roma minority population of Croatia--preliminary report.

A multidisciplinary anthropological and epidemiological pilot field study of the Bayash population living in 6 villages of the eastern Croatian region of Baranya has been performed in 2005/06. The Bayash (or Boyash) belong to the Roma minority population speaking a distinct archaic dialect of the Romanian language. Since the bone mineral density values in the Roma have not been explored so far and the prevalence of osteoporosis is unknown for this ethnic minority group a screening by means of the Sahara Hologic clinical bone sonometer has been performed on 232 voluntary participants (73 males and 159 females). The prevalence of osteoporosis (T-score <-2.5) in the Bayash aged 50 and older is found to be 9.1% in males and 34.4% in females, which is substantially higher than in the general population of Croatia. The prevalence of T-values ranging from -1 to -2.5 indicating osteopenia is found to be 63.6% in males and 45.3% in females, while T-values within the normal range are found only in 27.3% males and 20.3% females. In addition to the low bone mass in older subjects, the mean estimated bone mineral density in all age groups of Bayash men and women was lower in comparison to the manufacturer's reference ranges for European population of the same age. Since body size effects could not be declined, the reference values that would be appropriate for the Roma population should be further explored. The high estimated prevalence of developed osteoporosis calls for attention and the survey should also be extended to exploring the association of low bone mineral density with particular life style and reproductive factors present in this semi-sedentary Roma population.

Evaluation of Y-STR variation in Bosnian and Herzegovinian population.

Eight Y-STR polymorphisms (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393) were analyzed in the samples of 181 unrelated males from Bosnia and Herzegovinia. Observed STR allelic frequency pattern and locus diversity values in Bosnians and Herzegovinians correspond closer to neighboring southeastern European populations than previously reported (mostly western) European populations. One hundred and five haplotypes were identified and 78 haplotypes (74.3%) appeared in single copies. The most frequent haplotypes (DYS19-DYS385-DYS389I-DYS389II-DYS390-DYS391-DYS392-DYS393) were 16-14/15-13-31-24-11-11-13 (7.7%), 16-14/15-13-30-24-11-11-13 (7.7%) and 15-14/15-13-31-24-11-11-13 (5.5%). Total haplotype diversity was 0.9820 +/- 0.0040.

Population genetics of 8 Y chromosome STR loci in Macedonians and Macedonian Romani (Gypsy).

Eight Y chromosome short tandem repeat (STR) polymorphisms (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) were analyzed in Macedonians (n = 84) and Macedonian Romani ethnic group (n = 68). Observed allelic frequency distribution and locus diversity values in Macedonians correspond closer to neighboring southeastern European populations than (mostly) western European populations, whereas observed allelic frequency distribution and locus diversity values in Macedonian Romani, as expected based on their Asian (Indian) origin, differ from both neighboring southeastern and (mostly) western European populations. Sixty-six (78.57%) haplotypes appeared in single copies in Macedonians and 15 (22.06%) in Macedonian Romani. The most frequent Macedonian haplotypes (DYS19-DYS385-DYS389I-DYS389II-DYS390-DYS391-DYS392-DYS393) 16-14/15-13-31-24-11-11-13 and 13-16/18-13-30-24-10-11-13 were found in 7 and 6 copies, respectively. The most frequent Macedonian Romani haplotype 15-15/17-14-29-22-10-11-12 was found in 18 males. Total haplotype diversity was 0.9885 +/- 0.0058 (Macedonians) and 0.9008 +/- 0.0242 (Macedonian Romani).

High-resolution phylogenetic analysis of southeastern Europe traces major episodes of paternal gene flow among Slavic populations.

The extent and nature of southeastern Europe (SEE) paternal genetic contribution to the European genetic landscape were explored based on a high-resolution Y chromosome analysis involving 681 males from seven populations in the region. Paternal lineages present in SEE were compared with previously published data from 81 western Eurasian populations and 5,017 Y chromosome samples. The finding that five major haplogroups (E3b1, I1b* (xM26), J2, R1a, and R1b) comprise more than 70% of SEE total genetic variation is consistent with the typical European Y chromosome gene pool. However, distribution of major Y chromosomal lineages and estimated expansion signals clarify the specific role of this region in structuring of European, and particularly Slavic, paternal genetic heritage. Contemporary Slavic paternal gene pool, mostly characterized by the predominance of R1a and I1b* (xM26) and scarcity of E3b1 lineages, is a result of two major prehistoric gene flows with opposite directions: the post-Last Glacial Maximum R1a expansion from east to west, the Younger Dryas-Holocene I1b* (xM26) diffusion out of SEE in addition to subsequent R1a and I1b* (xM26) putative gene flows between eastern Europe and SEE, and a rather weak extent of E3b1 diffusion toward regions nowadays occupied by Slavic-speaking populations.

Y chromosome STR polymorphisms in a Serbian population sample.

Eight Y chromosome short tandem repeat (STR) polymorphisms (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) were analyzed in the sample of 114 unrelated males living in Serbia. A general STR allelic frequency pattern in Serbians corresponds to other European populations with the exception of loci DYS19, DYS389II and DYS385. Out of ninety identified haplotypes, 74 (64.91%) appeared in single copies. The most frequent haplotypes (DYS19-DYS385-DYS389I-DYS389II-DYS390-DYS391-DYS392-DYS393) 16-14/15-13-31-24-11-11-13 and 15-15/19-12-28-23-10-12-12 were found in four copies (3.51%). Total haplotype diversity was 0.9947+/-0.0021.

Genetic variation at nine short tandem repeat loci among islanders of the eastern Adriatic coast of Croatia.

We have analyzed the extent of genetic variation at nine autosomal short tandem repeat loci (D3S1358, VWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, D7S820) among six populations from Croatia: five distributed in the islands of the eastern Adriatic coast and one from the mainland. The purpose is to investigate the usefulness of these loci in detecting regional genetic differentiation in the studied populations. Significant heterogeneity among the island and mainland populations is revealed in the distributions of allele frequencies; however, the absolute magnitude of the coefficient of gene differentiation is small but significant. The summary measures of genetic variation, namely, heterozygosity, number of alleles, and allele size variance, do not indicate reduced genetic variation in the island populations compared to the mainland population. In contrast to the two measures of genetic variation, allele size variance and within-locus heterozygosity, the imbalance index (beta) indicates evidence of recent expansion of population sizes in all islands and in the mainland. High mutation rates of the studied loci together with local drift effects are likely explanations for interisland genetic variation and the observed lack of reduced genetic diversity among the island populations.

Holistic anthropological research of Hvar Islanders, Croatia--from parish registries to DNA studies in 33 years.

The complexity of interactions between hereditary, environmental and cultural factors in determining human phenotypes is often underestimated in biomedical research. In this paper, we present 33 years of holistic anthropological research that was being conducted since 1971 in the island of Hvar, Croatia. During this period, detailed characterization of migrations, demography, isonymy, linguistic differences, anthropometric traits (head and body dimensions), physiological (cardio-respiratory) properties, quantitative and qualitative dermatoglyphic traits, radiogrammetric metacarpal bone dimensions and genetic traits (classical antigens, HLA diversity, DNA short tandem repeat -STR, mitochondrial DNA and Y-chromosome polymorphisms) was performed. The analysis of this large collection of data using both model-bound and model-free approaches showed that the complexity underlying human biological traits may be considerably greater than generally assumed, which has important implications for design of future studies into genetic determinants of complex traits.

Y chromosome haplotypes in Albanian population from Kosovo.

Eight Y chromosome short tandem repeat (STR) polymorphisms (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393) were analyzed in the sample of 117 unrelated Albanian males living in Kosovo. A general STR allelic frequency pattern in the Albanian population from Kosovo corresponds to other European populations. Fourty six haplotypes were observed in single copy. The most frequent haplotypes were (DYS19-DYS385-DYS389I-DYS389II-DYS390-DYS391-DYS392-DYS393) 14-11/11-13-29-24-11-13-13 (10.26%), 14-14/17-12-28-24-10-11-12 (9.40%), 13-16/18-13-30-24-10-11-13 (9.40%), and 14-17/17-13-31-24-10-11-13 (9.40%).

Frequencies of mtDNA haplogroups in southeastern Europe--Croatians, Bosnians and Herzegovinians, Serbians, Macedonians and Macedonian Romani.

Mitochondrial DNA polymorphisms were analyzed in of 1,610 randomly chosen adult men from 11 different regions from southeastern Europe (Croatians, Bosnians and Herzegovinians, Serbians, Macedonians and Macedonian Romani). MtDNA HVS-I region together with RFLP sites diagnostic for main Euroasian and African mtDNA haplogroups were typed to determine haplogroup frequency distribution. The most frequent haplogroup in studied populations was H with the exception of Macedonian Romani among whom the most frequent were South Asian (Indian) specific variants of haplogroup M. The multidimensional scaling plot showed two clusters of populations and two outliers (Macedonian Romani and the most distant from mainland Croatian island of Korcula). The first cluster was formed by populations from three Croatian islands (Hvar, Krk and Brac) and the second cluster was formed by Macedonians, Serbians, Croatians from mainland and coast, Herzegovinians, Bosnians, Slovenians, Poles and Russians. The present analysis does not address a precise evaluation of phylogenetic relations of studied populations although some conclusions about historical migrations could be noticed. More extended conclusions will be possible after deeper phylogenetic and statistical analyses.