3000 years of solitude: extreme differentiation in the island isolates of Dalmatia, Croatia

Determinants of Human Asymmetry: Does Asymmetrical Retinal Vasculature Predict Asymmetry Elsewhere in the Body?

The aim of this study was to explore retinal vasculature asymmetry (ReVA) patterns in subjects from the islands of Vis and Korcula and the city of Split, Croatia. Asymmetry estimates were based on topographic image analysis of non-mydriatic retinal fundus photographs and compared with nine ophthalmic measurements, three Doppler-based pressure indices and eight frequencies of audiometry. ReVA was also correlated to the genomic runs of homozygosity (ROHs) and used in a Cox regression survival model, where we adjusted for the effects of sex, age and comorbidity. In 1873 subjects, ReVA estimates were significantly correlated with most ophthalmic asymmetry measures, less strongly with the ankle-brachial pressure index and only modestly with higher-amplitude audiometry asymmetries (lowest p = 0.020). ReVA was significantly correlated with the number of ROHs (r = 0.229, p < 0.001) but less strongly with the ROH length (r = 0.101, p < 0.001). The overlap of asymmetries was low, with only 107 subjects (5.7% of the total sample) who had two or more instances in which they were among the top 10%. Multiple asymmetries did not affect survival (HR = 0.74, 95% confidence intervals 0.45-1.22). Retinal vasculature asymmetry is a poor predictor of asymmetry elsewhere in the body. Despite its existence and apparent association with comorbidities, the observed extent of retinal vasculature asymmetry did not affect the lifespan in this population.

Genome-Wide Meta-Analysis Identifies Multiple Novel Rare Variants to Predict Common Human Infectious Diseases Risk

Infectious diseases still threaten global human health, and host genetic factors have been indicated as determining risk factors for observed variations in disease susceptibility, severity, and outcome. We performed a genome-wide meta-analysis on 4624 subjects from the 10,001 Dalmatians cohort, with 14 infection-related traits. Despite a rather small number of cases in some instances, we detected 29 infection-related genetic associations, mostly belonging to rare variants. Notably, the list included the genes CD28, INPP5D, ITPKB, MACROD2, and RSF1, all of which have known roles in the immune response. Expanding our knowledge on rare variants could contribute to the development of genetic panels that could assist in predicting an individual's life-long susceptibility to major infectious diseases. In addition, longitudinal biobanks are an interesting source of information for identifying the host genetic variants involved in infectious disease susceptibility and severity. Since infectious diseases continue to act as a selective pressure on our genomes, there is a constant need for a large consortium of biobanks with access to genetic and environmental data to further elucidate the complex mechanisms behind host-pathogen interactions and infectious disease susceptibility.

Do Islanders Have a More Reactive Behavioral Immune System? Social Cognitions and Preferred Interpersonal Distances During the COVID-19 Pandemic

Insular populations have traditionally drawn a lot of attention from epidemiologists as they provide important insights regarding transmission of infectious diseases and propagation of epidemics. There are numerous historical instances where isolated populations showed high morbidity once a new virus entered the population. Building upon that and recent findings that the activation of the behavioral immune system (BIS) depends both upon one's vulnerability and environmental context, we predicted that, during the COVID-19 pandemic, place of residence (island vs. mainland) explains a significant proportion of variance in preferred interpersonal distances, animosity toward strangers, and willingness to punish those who do not adhere to COVID-19 preventive measures. With 48 populated islands, Croatia provides a fruitful testing ground for this prediction. We also opted to explore relations among BIS-related variables (pathogen disgust, germ aversion, and perceived infectability) and social cognitions in a more natural context than has previously been done. The study was conducted online, on Croatian residents, during April and May 2020. As expected, the BIS variables contributed significantly to preferred interpersonal distances, negative emotions toward strangers, and willingness to punish those who do not adhere to COVID-19 preventive measures. Furthermore, our results showed that geographical location explained a significant amount of variance in preferred social (but not personal and intimate) distances and negative emotions toward foreigners. As Croatian islands are extremely frequent travel destinations, these differences between mainlanders and islanders cannot be explained by the lack of exposure to foreigners. Additionally, we found that scores on preferred interpersonal distances, pathogen disgust, and germ aversion were significantly higher compared to those obtained in Croatian samples before the COVID-19 pandemic. Furthermore, men scored higher in perceived infectability than before the COVID-19 pandemic, and women did not, which reflects the objectively higher risk of SARS-CoV-2 for men than for women. Taken together, our results support the notion that BIS is a highly adaptive and context-dependent response system, likely more reactive in more susceptible individuals.

The ethnobotany and biogeography of wild vegetables in the Adriatic islands

BACKGROUND

Archipelagos of islands have played an important role in shaping some of the paradigms of biology, including the theory of the evolution of species. Later, their importance in biology was further emphasised by the theory of island biogeography, which contributed to a better understanding of the shaping of species richness not only on real islands, but on isolated habitat islands as well. Although ethnobotany is a well-established discipline, patterns of knowledge about plant uses in archipelagos have never been quantitatively analysed, and the whole concept has been only briefly mentioned in the ethnobiological context. The aim of our study was to record which taxa of wild vegetables have been consumed in the Adriatic islands and to establish if such variables as island size, population size, flora or its isolation are correlated with the number of wild vegetables used.

METHODS

We interviewed 225 people (15 from each island).

RESULTS

Altogether, the use of 89 species of wild vegetables has been recorded. The largest number of wild vegetables is eaten on the islands of Korčula, Vis and Šolta, and the lowest on Ugljan, Cres and Dugi Otok. The studied independent variables had a small and statistically not significant effect on the wild vegetable list length. The most visible effect was an increasing trend from north-west to south-east, overrunning the typical biogeographical island patterns. Moreover, one of the large and well-populated islands, Korčula, showed an 'unusually' high level of wild vegetable use. We hypothesise that the current use of so many species on this island has been maintained by the inhabitants' awareness that they are the holders of relic knowledge, an awareness reiterated by ethnographic and popular publications, as well as a strong history of famine. The most interesting edible species used in the Adriatic islands are Bunium alpinum, Cytinus hypocystis (both mainly on Pašman), Lotus edulis (on Vis) and Posidonia oceanica (on Vis and Korčula).

CONCLUSIONS

The recorded relationships between the demographic and geographical features of the islands were statistically not significant. We assume that cultural and historical factors diversifying the use of plants in particular islands are stronger than the above-mentioned measurable variables.

Neuroticism and pain catastrophizing aggravate response to pain in healthy adults: an experimental study

Background

The aim of this study was to investigate the association between neuroticism, pain catastrophizing, and experimentally induced pain threshold and pain tolerance in a healthy adult sample from two regions of the country of Croatia: the island of Korcula and city of Split.

Methods

A total of 1,322 participants were enrolled from the Island of Korcula (n = 824) and the city of Split (n = 498). Participants completed a self-reported personality measure Eysenck Personality Questionnaire (EPQ) and pain catastrophizing questionnaire Pain Catastrophizing Scale (PCS), followed by a mechanical pain pressure threshold and tolerance test. We have explored the mediating role of catastrophizing in the relationship between neuroticism and pain intensity.

Results

The results showed that pain catastrophizing partially mediated the relationship between neuroticism and pain intensity, suggesting the importance of pain catastrophizing in increasing vulnerability to pain. The results also indicated gender-related differences, marked by the higher pain threshold and tolerance in men.

Conclusions

This study adds to the understanding of the complex interplay between personality and pain, by providing a better understanding of such mechanisms in healthy adults.

Whole-exome sequencing in an isolated population from the Dalmatian island of Vis

We have whole-exome sequenced 176 individuals from the isolated population of the island of Vis in Croatia in order to describe exonic variation architecture. We found 290 577 single nucleotide variants (SNVs), 65% of which are singletons, low frequency or rare variants. A total of 25 430 (9%) SNVs are novel, previously not catalogued in NHLBI GO Exome Sequencing Project, UK10K-Generation Scotland, 1000Genomes Project, ExAC or NCBI Reference Assembly dbSNP. The majority of these variants (76%) are singletons. Comparable to data obtained from UK10K-Generation Scotland that were sequenced and analysed using the same protocols, we detected an enrichment of potentially damaging variants (non-synonymous and loss-of-function) in the low frequency and common variant categories. On average 115 (range 93–140) genotypes with loss-of-function variants, 23 (15–34) of which were homozygous, were identified per person. The landscape of loss-of-function variants across an exome revealed that variants mainly accumulated in genes on the xenobiotic-related pathways, of which majority coded for enzymes. The frequency of loss-of-function variants was additionally increased in Vis runs of homozygosity regions where variants mainly affected signalling pathways. This work confirms the isolate status of Vis population by means of whole-exome sequence and reveals the pattern of loss-of-function mutations, which resembles the trails of adaptive evolution that were found in other species. By cataloguing the exomic variants and describing the allelic structure of the Vis population, this study will serve as a valuable resource for future genetic studies of human diseases, population genetics and evolution in this population.

Genomic prediction of complex human traits: relatedness, trait architecture and predictive meta-models

We explore the prediction of individuals' phenotypes for complex traits using genomic data. We compare several widely used prediction models, including Ridge Regression, LASSO and Elastic Nets estimated from cohort data, and polygenic risk scores constructed using published summary statistics from genome-wide association meta-analyses (GWAMA). We evaluate the interplay between relatedness, trait architecture and optimal marker density, by predicting height, body mass index (BMI) and high-density lipoprotein level (HDL) in two data cohorts, originating from Croatia and Scotland. We empirically demonstrate that dense models are better when all genetic effects are small (height and BMI) and target individuals are related to the training samples, while sparse models predict better in unrelated individuals and when some effects have moderate size (HDL). For HDL sparse models achieved good across-cohort prediction, performing similarly to the GWAMA risk score and to models trained within the same cohort, which indicates that, for predicting traits with moderately sized effects, large sample sizes and familial structure become less important, though still potentially useful. Finally, we propose a novel ensemble of whole-genome predictors with GWAMA risk scores and demonstrate that the resulting meta-model achieves higher prediction accuracy than either model on its own. We conclude that although current genomic predictors are not accurate enough for diagnostic purposes, performance can be improved without requiring access to large-scale individual-level data. Our methodologically simple meta-model is a means of performing predictive meta-analysis for optimizing genomic predictions and can be easily extended to incorporate multiple population-level summary statistics or other domain knowledge.

Socioeconomic inequalities show remarkably poor association with health and disease in Southern Croatia

OBJECTIVES

This study aimed at investigating the association of socioeconomic status and health outcomes in populations of the two remote Croatian islands and one coastal city.

METHODS

Medical history and survey information were used to create 33 variables that were analysed using logistic regression. The population from the island of Vis was followed up and mortality data were used to calculate hazard ratios using Cox regression.

RESULTS

Socioeconomic inequalities were poorly associated with health and disease indices. In the matrix of 33 outcome variables and 13 socioeconomic predictor classes, only 10 associations were significant at the level of P < 0.001. None of the associations was replicated across samples. We did not detect the association of any socioeconomic estimate with mortality data for the island of Vis.

CONCLUSIONS

Homogenous island populations were expected to have greater levels of social homogeneity and consequently less expressed inequalities in health. The lack of stronger association in the urban population of Split is likely the result of the mechanisms that persisted from the former communist regime and high level of retained formal and informal social support.

High-Performance Mixed Models Based Genome-Wide Association Analysis with omicABEL software

To raise the power of genome-wide association studies (GWAS) and avoid false-positive results in structured populations, one can rely on mixed model based tests. When large samples are used, and when multiple traits are to be studied in the 'omics' context, this approach becomes computationally challenging. Here we consider the problem of mixed-model based GWAS for arbitrary number of traits, and demonstrate that for the analysis of single-trait and multiple-trait scenarios different computational algorithms are optimal. We implement these optimal algorithms in a high-performance computing framework that uses state-of-the-art linear algebra kernels, incorporates optimizations, and avoids redundant computations, increasing throughput while reducing memory usage and energy consumption. We show that, compared to existing libraries, our algorithms and software achieve considerable speed-ups. The OmicABEL software described in this manuscript is available under the GNU GPL v. 3 license as part of the GenABEL project for statistical genomics at http: //www.genabel.org/packages/OmicABEL.

Using population isolates in genetic association studies

The use of genetically isolated populations can empower next-generation association studies. In this review, we discuss the advantages of this approach and review study design and analytical considerations of genetic association studies focusing on isolates. We cite successful examples of using population isolates in association studies and outline potential ways forward.

The association between galactosylation of immunoglobulin G and body mass index

OBJECTIVE

Obesity is becoming a fast-growing health problem worldwide. Glycosylation of proteins and their variations significantly affect protein structure and function, thus altering numerous physiological and pathophysiological cellular processes. Since plasma glycans were significantly associated with body mass index (BMI) in both Croatian and Chinese populations, the study evaluated the association between immunoglobulin G (IgG) glycome, which is closer to biological function, and BMI.

METHOD

The study included individuals from two Croatian Adriatic islands, Vis and Korčula, and individuals from Northern Scottish Orkney Islands. A hydrophilic interaction chromatography on Waters BEH Glycan chromatography column was used to analyze N-glycans attached to IgG in plasma samples from a total of 3515 individuals.

RESULTS

A small but significant positive correlation between BMI and the level of neutral glycans without galactoses was detected. After taking into account the influence of age and gender, correlation coefficients indicated that BMI was responsible for up to 2.0% of variation in the level of neutral glycans without galactoses. Furthermore, after adjusting the effects of age and gender, the level of neutral glycans with two terminal galactoses was negatively associated with BMI in analyzed sample groups, suggesting that BMI could be responsible for up to 3.2% of variation in this glycan feature.

CONCLUSION

Our study is the first large-scale study to indicate the association of BMI and changes in IgG galactosylation. The observed loss of galactose which is associated with increased BMI might be related to chronic inflammation that accompanies the development of obesity.

Inference of identity by descent in population isolates and optimal sequencing studies

In an isolated population, individuals are likely to share large genetic regions inherited from common ancestors. Identity by descent (IBD) can be inferred from SNP genotypes, which is useful in a number of applications, including identifying genetic variants influencing complex disease risk, and planning efficient cohort-sequencing strategies. We present ANCHAP--a method for detecting IBD in isolated populations. We compare accuracy of the method against other long-range and local phasing methods, using parent-offspring trios. In our experiments, we show that ANCHAP performs similarly as the other long-range method, but requires an order-of-magnitude less computational resources. A local phasing model is able to achieve similar sensitivity, but only at the cost of higher false discovery rates. In some regions of the genome, the studied individuals share haplotypes particularly often, which hints at the history of the populations studied. We demonstrate the method using SNP genotypes from three isolated island populations, as well as in a cohort of unrelated individuals. In samples from three isolated populations of around 1000 individual each, an average individual shares a haplotype at a genetic locus with 9-12 other individuals, compared with only 1 individual within the non-isolated population. We describe an application of ANCHAP to optimally choose samples in resequencing studies. We find that with sample sizes of 1000 individuals from an isolated population genotyped using a dense SNP array, and with 20% of these individuals sequenced, 65% of sequences of the unsequenced subjects can be partially inferred.

Genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the biosynthesis of long-chain omega-3 and omega-6 fatty acids

Omega-3 and omega-6 long-chain polyunsaturated fatty acids (LC-PUFAs) are essential for the development and function of the human brain. They can be obtained directly from food, e.g., fish, or synthesized from precursor molecules found in vegetable oils. To determine the importance of genetic variability to fatty-acid biosynthesis, we studied FADS1 and FADS2, which encode rate-limiting enzymes for fatty-acid conversion. We performed genome-wide genotyping (n = 5,652 individuals) and targeted resequencing (n = 960 individuals) of the FADS region in five European population cohorts. We also analyzed available genomic data from human populations, archaic hominins, and more distant primates. Our results show that present-day humans have two common FADS haplotypes-defined by 28 closely linked SNPs across 38.9 kb-that differ dramatically in their ability to generate LC-PUFAs. No independent effects on FADS activity were seen for rare SNPs detected by targeted resequencing. The more efficient, evolutionarily derived haplotype appeared after the lineage split leading to modern humans and Neanderthals and shows evidence of positive selection. This human-specific haplotype increases the efficiency of synthesizing essential long-chain fatty acids from precursors and thereby might have provided an advantage in environments with limited access to dietary LC-PUFAs. In the modern world, this haplotype has been associated with lifestyle-related diseases, such as coronary artery disease.

Genome-wide analysis of epistasis in body mass index using multiple human populations

We surveyed gene–gene interactions (epistasis) in human body mass index (BMI) in four European populations (n<1200) via exhaustive pair-wise genome scans where interactions were computed as F ratios by testing a linear regression model fitting two single-nucleotide polymorphisms (SNPs) with interactions against the one without. Before the association tests, BMI was corrected for sex and age, normalised and adjusted for relatedness. Neither single SNPs nor SNP interactions were genome-wide significant in either cohort based on the consensus threshold (P=5.0E−08) and a Bonferroni corrected threshold (P=1.1E−12), respectively. Next we compared sub genome-wide significant SNP interactions (P<5.0E−08) across cohorts to identify common epistatic signals, where SNPs were annotated to genes to test for gene ontology (GO) enrichment. Among the epistatic genes contributing to the commonly enriched GO terms, 19 were shared across study cohorts of which 15 are previously published genome-wide association loci, including CDH13 (cadherin 13) associated with height and SORCS2 (sortilin-related VPS10 domain containing receptor 2) associated with circulating insulin-like growth factor 1 and binding protein 3. Interactions between the 19 shared epistatic genes and those involving BMI candidate loci (P<5.0E−08) were tested across cohorts and found eight replicated at the SNP level (P<0.05) in at least one cohort, which were further tested and showed limited replication in a separate European population (n>5000). We conclude that genome-wide analysis of epistasis in multiple populations is an effective approach to provide new insights into the genetic regulation of BMI but requires additional efforts to confirm the findings.

Influence of evolutionary forces and demographic processes on the genetic structure of three Croatian populations: a maternal perspective

BACKGROUND

Many Croatian islands are examples of genetic isolates, with low level of heterozygosity and high level of inbreeding, due to practice of endogamy.

AIM

The aim was to study the genetic structure of two insular and one mainland population through high-resolution phylogenetic analysis of mitochondrial DNA (mtDNA).

SUBJECTS AND METHODS

MtDNA polymorphisms were explored in 300 unrelated individuals from Mljet, Lastovo and the coastal city of Dubrovnik, based on SNP polymorphisms.

RESULTS

All mtDNA haplogroups found in the sample were of typical European origin. However, the frequency distribution of their subclades differed significantly from other Croatian and European populations. MtDNA haplotype analysis revealed only two possible founder lineages on Mljet and six on Lastovo, accounting for almost half of the sample on both islands. The island of Mljet also has the lowest reported haplotype and nucleotide diversity among Croatian isolates and the island of Lastovo, a new sublineage of a usually quite rare U1b clade.

CONCLUSION

The results can be explained by the effect evolutionary forces have on genetic structure, which is in line with the specific demographic histories of the islands. An additional research value of these two island isolates is the appearance of certain Mendelian disorders, highlighting their importance in epidemiological studies.

Characterisation of genome-wide association epistasis signals for serum uric acid in human population isolates

Genome-wide association (GWA) studies have identified a number of loci underlying variation in human serum uric acid (SUA) levels with the SLC2A9 gene having the largest effect identified so far. Gene-gene interactions (epistasis) are largely unexplored in these GWA studies. We performed a full pair-wise genome scan in the Italian MICROS population (n = 1201) to characterise epistasis signals in SUA levels. In the resultant epistasis profile, no SNP pairs reached the Bonferroni adjusted threshold for the pair-wise genome-wide significance. However, SLC2A9 was found interacting with multiple loci across the genome, with NFIA-SLC2A9 and SLC2A9-ESRRAP2 being significant based on a threshold derived for interactions between GWA significant SNPs and the genome and jointly explaining 8.0% of the phenotypic variance in SUA levels (3.4% by interaction components). Epistasis signal replication in a CROATIAN population (n = 1772) was limited at the SNP level but improved dramatically at the gene ontology level. In addition, gene ontology terms enriched by the epistasis signals in each population support links between SUA levels and neurological disorders. We conclude that GWA epistasis analysis is useful despite relatively low power in small isolated populations.

Copy number variation across European populations

Genome analysis provides a powerful approach to test for evidence of genetic variation within and between geographical regions and local populations. Copy number variants which comprise insertions, deletions and duplications of genomic sequence provide one such convenient and informative source. Here, we investigate copy number variants from genome wide scans of single nucleotide polymorphisms in three European population isolates, the island of Vis in Croatia, the islands of Orkney in Scotland and the South Tyrol in Italy. We show that whereas the overall copy number variant frequencies are similar between populations, their distribution is highly specific to the population of origin, a finding which is supported by evidence for increased kinship correlation for specific copy number variants within populations.

Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits

We have used targeted genomic sequencing of high-complexity DNA pools based on long-range PCR and deep DNA sequencing by the SOLiD technology. The method was used for sequencing of 286 kb from four chromosomal regions with quantitative trait loci (QTL) influencing blood plasma lipid and uric acid levels in DNA pools of 500 individuals from each of five European populations. The method shows very good precision in estimating allele frequencies as compared with individual genotyping of SNPs (r(2) = 0.95, P < 10(-16)). Validation shows that the method is able to identify novel SNPs and estimate their frequency in high-complexity DNA pools. In our five populations, 17% of all SNPs and 61% of structural variants are not available in the public databases. A large fraction of the novel variants show a limited geographic distribution, with 62% of the novel SNPs and 59% of novel structural variants being detected in only one of the populations. The large number of population-specific novel SNPs underscores the need for comprehensive sequencing of local populations in order to identify the causal variants of human traits.

Does inbreeding affect N-glycosylation of human plasma proteins?

Inbreeding depression and heterosis are the two ends of phenotypic changes defined by the genome-wide homozygosity. The aim of this study was to investigate the association of genetic marker-based homozygosity estimates with 46 N-glycan features measured in human plasma. The study was based on a total of 2,341 subjects, originating from three isolated island communities in Croatia (Vis and Korcula islands) and Scotland (Orkney Islands). Inbreeding estimates were associated with an increase in tetrantennary and tetrasialylated glycans, and a decrease in digalactosylated glycans (P < 0.001). The strength of this association was proportional to the mean cohort-based inbreeding coefficient. Increase in tetraantennary glycans is known to be associated with various tumours and their association with inbreeding might be one of the mechanisms underlying the increased prevalence of tumours reported in some human isolated populations. Further studies are thus merited in order to confirm the association of inbreeding with changes in glycan profiles in other plant and animal populations, thus attempting to establish if glycosylation could indeed be involved in mediation of some phenotypic changes described in inbred and outbred organisms.

Interactions between genetic variants in glucose transporter type 9 (SLC2A9) and dietary habits in serum uric acid regulation

AIM

To investigate possible interactions between genetic variants in glucose transporter type 9 (SLC2A9) gene and dietary habits in serum uric acid regulation.

METHODS

Participants for this study were recruited from two isolated Croatian island communities of Vis (n=918) and Korcula (n=898). Three single nucleotide polymorphisms (SNP) from the SLC2A9 gene (rs1014290, rs6449213, rs737267) were correlated with dietary habits and uric acid.

RESULTS

A significant decrease in uric acid levels was recorded with increasing consumption of milk, sour cream, duck and turkey, and eggs. The only significant interaction was found between potato consumption and rs737267 and a near-significant interaction was found between soft drinks and rs1014290 (interaction P=0.068). Increased consumption of soft drinks interacting with the TT genotype at rs1014290 increased serum uric acid. No significant interactions were observed between food products consumption and rs6449213.

CONCLUSION

There is a certain extent of interaction between SLC2A9 and dietary patterns in serum uric acid determination. The metabolic effect of soft drinks seems to be determined by the underlying genotype of rs1014290.

Predictive value of 8 genetic loci for serum uric acid concentration

AIM

To investigate the value of genomic information in prediction of individual serum uric acid concentrations.

METHODS

Three population samples were investigated: from isolated Adriatic island communities of Vis (n=980) and Korcula (n=944), and from general population of the city of Split (n=507). Serum uric acid concentration was correlated with the genetic risk score based on 8 previously described genes: PDZK1, GCKR, SLC2A9, ABCG2, LRRC16A, SLC17A1, SLC16A9, and SLC22A12, represented by a total of 16 single-nucleotide polymorphisms (SNP). The data were analyzed using classification and regression tree (CART) and general linear modeling.

RESULTS

The most important variables for uric acid prediction with CART were genetic risk score in men and age in women. The percent of variance for any single SNP in predicting serum uric acid concentration varied from 0.0%-2.0%. The use of genetic risk score explained 0.1%-2.5% of uric acid variance in men and 3.9%-4.9% in women. The highest percent of variance was obtained when age, sex, and genetic risk score were used as predictors, with a total of 30.9% of variance in pooled analysis.

CONCLUSION

Despite overall low percent of explained variance, uric acid seems to be among the most predictive human quantitative traits based on the currently available SNP information. The use of genetic risk scores is a valuable approach in genetic epidemiology and increases the predictability of human quantitative traits based on genomic information compared with single SNP approach.

Linkage and genome-wide association analysis of obesity-related phenotypes: association of weight with the MGAT1 gene

As major risk-factors for diabetes and cardiovascular diseases, the genetic contribution to obesity-related traits has been of interest for decades. Recently, a limited number of common genetic variants, which have replicated in different populations, have been identified. One approach to increase the statistical power in genetic mapping studies is to focus on populations with increased levels of linkage disequilibrium (LD) and reduced genetic diversity. We have performed joint linkage and genome-wide association analyses for weight and BMI in 3,448 (linkage) and 3,925 (association) partly overlapping healthy individuals from five European populations. A total of four chromosomal regions (two for weight and two for BMI) showed suggestive linkage (lod >2.69) either in one of the populations or in the joint data. At the genome-wide level (nominal P < 1.6 x 10(-7), Bonferroni-adjusted P < 0.05) one single-nucleotide polymorphism (SNP) (rs12517906) (nominal P = 7.3 x 10(-8)) was associated with weight, whereas none with BMI. The SNP associated with weight is located close to MGAT1. The monoacylglycerol acyltransferase (MGAT) enzyme family is known to be involved in dietary fat absorption. There was no overlap between the linkage regions and the associated SNPs. Our results show that genetic effects influencing weight and BMI are shared across diverse European populations, even though some of these populations have experienced recent population bottlenecks and/or been affected by genetic drift. The analysis enabled us to identify a new candidate gene, MGAT1, associated with weight in women.

A meta-analysis of genome-wide data from five European isolates reveals an association of COL22A1, SYT1, and GABRR2 with serum creatinine level

BACKGROUND

Serum creatinine (S CR) is the most important biomarker for a quick and non-invasive assessment of kidney function in population-based surveys. A substantial proportion of the inter-individual variability in S CR level is explicable by genetic factors.

METHODS

We performed a meta-analysis of genome-wide association studies of S CR undertaken in five population isolates ('discovery cohorts'), all of which are part of the European Special Population Network (EUROSPAN) project. Genes showing the strongest evidence for an association with SCR (candidate loci) were replicated in two additional population-based samples ('replication cohorts').

RESULTS

After the discovery meta-analysis, 29 loci were selected for replication. Association between SCR level and polymorphisms in the collagen type XXII alpha 1 (COL22A1) gene, on chromosome 8, and in the synaptotagmin-1 (SYT1) gene, on chromosome 12, were successfully replicated in the replication cohorts (p value = 1.0 x 10(-6) and 1.7 x 10(-4), respectively). Evidence of association was also found for polymorphisms in a locus including the gamma-aminobutyric acid receptor rho-2 (GABRR2) gene and the ubiquitin-conjugating enzyme E2-J1 (UBE2J1) gene (replication p value = 3.6 x 10(-3)). Previously reported findings, associating glomerular filtration rate with SNPs in the uromodulin (UMOD) gene and in the schroom family member 3 (SCHROOM3) gene were also replicated.

CONCLUSIONS

While confirming earlier results, our study provides new insights in the understanding of the genetic basis of serum creatinine regulatory processes. In particular, the association with the genes SYT1 and GABRR2 corroborate previous findings that highlighted a possible role of the neurotransmitters GABAA receptors in the regulation of the glomerular basement membrane and a possible interaction between GABAA receptors and synaptotagmin-I at the podocyte level.

Comparison of participant information and informed consent forms of five European studies in genetic isolated populations

Family-based research in genetically isolated populations is an effective approach for identifying loci influencing variation in disease traits. In common with all studies in humans, those in genetically isolated populations need ethical approval; however, existing ethical frameworks may be inadequate to protect participant privacy and confidentiality and to address participants' information needs in such populations. Using the ethical-legal guidelines of the Council for International Organizations of Medical Sciences (CIOMS) as a template, we compared the participant information leaflets and consent forms of studies in five European genetically isolated populations to identify additional information that should be incorporated into information leaflets and consent forms to guarantee satisfactorily informed consent. We highlight the additional information that participants require on the research purpose and the reasons why their population was chosen; on the potential risks and benefits of participation; on the opportunities for benefit sharing; on privacy; on the withdrawal of consent and on the disclosure of genetic data. This research raises some important issues that should be addressed properly and identifies relevant types of information that should be incorporated into information leaflets for this type of study.

Comparative assessment of methods for estimating individual genome-wide homozygosity-by-descent from human genomic data

Background

Genome-wide homozygosity estimation from genomic data is becoming an increasingly interesting research topic. The aim of this study was to compare different methods for estimating individual homozygosity-by-descent based on the information from human genome-wide scans rather than genealogies. We considered the four most commonly used methods and investigated their applicability to single-nucleotide polymorphism (SNP) data in both a simulation study and by using the human genotyped data. A total of 986 inhabitants from the isolated Island of Vis, Croatia (where inbreeding is present, but no pedigree-based inbreeding was observed at the level of F > 0.0625) were included in this study. All individuals were genotyped with the Illumina HumanHap300 array with 317,503 SNP markers.

Results

Simulation data suggested that multi-point FEstim is the method most strongly correlated to true homozygosity-by-descent. Correlation coefficients between the homozygosity-by-descent estimates were high but only for inbred individuals, with nearly absolute correlation between single-point measures.

Conclusions

Deciding who is really inbred is a methodological challenge where multi-point approaches can be very helpful once the set of SNP markers is filtered to remove linkage disequilibrium. The use of several different methodological approaches and hence different homozygosity measures can help to distinguish between homozygosity-by-state and homozygosity-by-descent in studies investigating the effects of genomic autozygosity on human health.

Genetic comparison of a Croatian isolate and CEPH European founders

Human isolates have been postulated as a good resource for the identification of QTL due to reduced genetic diversity and a more homogeneous environment. Isolates may also have increased linkage disequilibrium (LD) due to small effective population size and, either loss or increase in frequency of alleles that are rare in the general population from which they originate. Here we investigate the difference in allele and genotype frequencies, LD and homozygous tracts between an isolate-several villages from the island of Vis in Croatia-and an outbred population of European origin: the Hapmap CEPH founders. Using the HumanHap300 v1 Genotyping BeadChip, we show that our population does not differ greatly from the reference CEU outbred population despite having a slightly higher proportion of monomorphic loci, a slightly higher long-range LD, and a greater proportion of individuals with long homozygous tracts. We conclude that genotyping arrays should perform equally well in our isolate as in outbred European populations for disease mapping studies and that SNP-trait associations discovered in our well-characterized Croatian isolate should be valid in the general European population from which they descend.

Common variants in SLC17A3 gene affect intra-personal variation in serum uric acid levels in longitudinal time series

AIM

To investigate whether intra-personal variation in serum uric acid concentration is influenced by genes that were described to be associated with serum uric acid levels in cross-sectional studies.

METHODS

The study included 92 participants from the isolated community of the Croatian island of Vis. For each participant, two uric acid concentration measurements were available, one from 2002 and one from 2003. Changes in uric acid concentration were correlated with a set of 8 genes known to affect it: PDZK1, GCKR, SLC2A9, ABCG2, LRRC16A, SLC17A3, SLC16A9, and SLC22A12.

RESULTS

Thirteen participants (14%) had uric acid concentration change greater than 130 micromol/L. Greater variability of uric acid concentration was recorded in women (coefficient of variation 49% vs 12% in men). Two SNPs belonging to SLC17A3 gene (rs9393672 and rs942379) yielded significant association with serum uric acid concentration changes in women. These two single-nucleotide polymorphisms (SNP) explained 0.2%-1.3% of variance for 2002 or 2003 uric acid measurement and 1.1%-1.8% of variance for the average value of these two measurements.

CONCLUSIONS

Repeated measurements offer a possibility to enrich the percent of explained variance and contribute to the understanding of the "missing heritability" concept. Although a number of genes have been shown to affect serum uric acid concentration, SLC17A3 seems to have a major role in determination of serum uric acid repeated measurements variation.

Association of nephrolithiasis and gene for glucose transporter type 9 (SLC2A9): study of 145 patients

AIM

To investigate the association of nephrolithiasis and solute carrier family 2, facilitated glucose transporter, member 9 (SLC2A9), also known as glucose transporter type 9, Glut9.

METHODS

A total of 145 participants were recruited in the period April-October 2008 from the Department of Mineral Research of the Medical School Osijek, Osijek, Croatia; 58 (40%) had confirmed nephrolithiasis and 87 (60%) were asymptomatic. Four single nucleotide polymorphisms (SNP) from the SLC2A9 gene were genotyped in both groups (rs733175, rs6449213, rs1014290, and rs737267).

RESULTS

There was a weak but significant association of all 4 SNPs and nephrolithiasis (P=0.029 for rs733175; P=0.006 for rs6449213; P=0.020 for rs1014290, and P=0.011 for rs737267). Logistic regression in an age- and sex-adjusted model suggested that genotype C/T for rs6449213 had odds ratio for nephrolithiasis of 2.89 (95% confidence interval 1.13-7.40). This SNP explained a total of 4.4% of nephrolithiasis variance.

CONCLUSION

Development of nephrolithiasis may be associated with SLC2A9 gene. Further studies are needed to clarify the role of SLC2A9 gene as a link between uric acid and nephrolithiasis.

Modeling of environmental effects in genome-wide association studies identifies SLC2A2 and HP as novel loci influencing serum cholesterol levels

Genome-wide association studies (GWAS) have identified 38 larger genetic regions affecting classical blood lipid levels without adjusting for important environmental influences. We modeled diet and physical activity in a GWAS in order to identify novel loci affecting total cholesterol, LDL cholesterol, HDL cholesterol, and triglyceride levels. The Swedish (SE) EUROSPAN cohort (N(SE) = 656) was screened for candidate genes and the non-Swedish (NS) EUROSPAN cohorts (N(NS) = 3,282) were used for replication. In total, 3 SNPs were associated in the Swedish sample and were replicated in the non-Swedish cohorts. While SNP rs1532624 was a replication of the previously published association between CETP and HDL cholesterol, the other two were novel findings. For the latter SNPs, the p-value for association was substantially improved by inclusion of environmental covariates: SNP rs5400 (p(SE,unadjusted) = 3.6 x 10(-5), p(SE,adjusted) = 2.2 x 10(-6), p(NS,unadjusted) = 0.047) in the SLC2A2 (Glucose transporter type 2) and rs2000999 (p(SE,unadjusted) = 1.1 x 10(-3), p(SE,adjusted) = 3.8 x 10(-4), p(NS,unadjusted) = 0.035) in the HP gene (Haptoglobin-related protein precursor). Both showed evidence of association with total cholesterol. These results demonstrate that inclusion of important environmental factors in the analysis model can reveal new genetic susceptibility loci.

Comparing population structure as inferred from genealogical versus genetic information

Algorithms for inferring population structure from genetic data (ie, population assignment methods) have shown to effectively recognize genetic clusters in human populations. However, their performance in identifying groups of genealogically related individuals, especially in scanty-differentiated populations, has not been tested empirically thus far. For this study, we had access to both genealogical and genetic data from two closely related, isolated villages in southern Italy. We found that nearly all living individuals were included in a single pedigree, with multiple inbreeding loops. Despite F(st) between villages being a low 0.008, genetic clustering analysis identified two clusters roughly corresponding to the two villages. Average kinship between individuals (estimated from genealogies) increased at increasing values of group membership (estimated from the genetic data), showing that the observed genetic clusters represent individuals who are more closely related to each other than to random members of the population. Further, average kinship within clusters and F(st) between clusters increases with increasingly stringent membership threshold requirements. We conclude that a limited number of genetic markers is sufficient to detect structuring, and that the results of genetic analyses faithfully mirror the structuring inferred from detailed analyses of population genealogies, even when F(st) values are low, as in the case of the two villages. We then estimate the impact of observed levels of population structure on association studies using simulated data.

Genetic determinants of circulating sphingolipid concentrations in European populations

Sphingolipids have essential roles as structural components of cell membranes and in cell signalling, and disruption of their metabolism causes several diseases, with diverse neurological, psychiatric, and metabolic consequences. Increasingly, variants within a few of the genes that encode enzymes involved in sphingolipid metabolism are being associated with complex disease phenotypes. Direct experimental evidence supports a role of specific sphingolipid species in several common complex chronic disease processes including atherosclerotic plaque formation, myocardial infarction (MI), cardiomyopathy, pancreatic beta-cell failure, insulin resistance, and type 2 diabetes mellitus. Therefore, sphingolipids represent novel and important intermediate phenotypes for genetic analysis, yet little is known about the major genetic variants that influence their circulating levels in the general population. We performed a genome-wide association study (GWAS) between 318,237 single-nucleotide polymorphisms (SNPs) and levels of circulating sphingomyelin (SM), dihydrosphingomyelin (Dih-SM), ceramide (Cer), and glucosylceramide (GluCer) single lipid species (33 traits); and 43 matched metabolite ratios measured in 4,400 subjects from five diverse European populations. Associated variants (32) in five genomic regions were identified with genome-wide significant corrected p-values ranging down to 9.08x10(-66). The strongest associations were observed in or near 7 genes functionally involved in ceramide biosynthesis and trafficking: SPTLC3, LASS4, SGPP1, ATP10D, and FADS1-3. Variants in 3 loci (ATP10D, FADS3, and SPTLC3) associate with MI in a series of three German MI studies. An additional 70 variants across 23 candidate genes involved in sphingolipid-metabolizing pathways also demonstrate association (p = 10(-4) or less). Circulating concentrations of several key components in sphingolipid metabolism are thus under strong genetic control, and variants in these loci can be tested for a role in the development of common cardiovascular, metabolic, neurological, and psychiatric diseases.

Genome-wide association study of anthropometric traits in Korcula Island, Croatia

AIM

To identify genetic variants underlying six anthropometric traits: body height, body weight, body mass index, brachial circumference, waist circumference, and hip circumference, using a genome-wide association study.

METHODS

The study was carried out in the isolated population of the island of Korcula, Croatia, with 898 adult examinees who participated in the larger DNA-based genetic epidemiological study in 2007. Anthropometric measurements followed standard internationally accepted procedures. Examinees were genotyped using HumanHap 370CNV chip by Illumina, with a genome-wide scan containing 316730 single nucleotide polymorphisms (SNP).

RESULTS

A total of 11 SNPs were associated with the investigated traits at the level of P<10(-5), with one SNP (rs7792939 in gene zinc finger protein 498, ZNF498) associated with body weight, hip circumference, and brachial circumference (P=3.59-5.73 x 10(-6)), and another one (rs157350 in gene delta-sarcoglycan, SGCD) with both brachial and hip circumference (P=3.70-6.08 x 10(-6). Variants in CRIM1, a gene regulating delivery of bone morphogenetic proteins to the cell surface, and ITGA1, involved in the regulation of mesenchymal stem cell proliferation and cartilage production, were also associated with brachial circumference (P=7.82 and 9.68 x 10(-6), respectively) and represent interesting functional candidates. Other associations involved those between genes SEZ6L2 and MAX and waist circumference, XTP6 and brachial circumference, and AMPA1/GRIA1 and height.

CONCLUSION

Although the study was underpowered for the reported associations to reach formal threshold of genome-wide significance under the assumption of independent multiple testing, the consistency of association between the 2 variants and a set of anthropometric traits makes CRIM1 and ITGA1 highly interesting for further replication and functional follow-up. Increased linkage disequilibrium between the used markers in an isolated population makes the formal significance threshold overly stringent, and changed allele frequencies in isolate population may contribute to identifying variants that would not be easily identified in large outbred populations.

Common variant in myocilin gene is associated with high myopia in isolated population of Korcula Island, Croatia

AIM

To study the association between genetic variants in myocilin and collagen type I alpha 1 genes and high myopia in an isolated island population.

METHODS

A total of 944 examinees from the genetic epidemiology study conducted on the island of Korcula, Croatia, were included in the study. We selected 2 short nucleotide polymorphisms (SNP) available in our genome-wide scan set of SNPs that were previously associated with high myopia and used them to replicate previous claims of possible association.

RESULTS

Nineteen cases of high myopia, defined as the refraction of </=-6.00 diopters, were identified and included in the analysis. We showed that rs2075555 in the COL1A1 gene was not associated with high myopia. In contrast, rs2421853 in the myocilin gene was significantly associated in both bivariate (P=0.006) and age- and sex-adjusted analysis (P=0.049).

CONCLUSION

Myocilin seems to be a very strong candidate for explaining some of the pathophysiological pathways leading to the development of both glaucoma and high myopia. As our finding was obtained in a relatively under-powered sample, further research and replication of these results is needed.

Genome-wide association study of biochemical traits in Korcula Island, Croatia

AIM

To identify genetic variants underlying biochemical traits--total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, triglycerides, uric acid, albumin, and fibrinogen, in a genome-wide association study in an isolated population where rare variants of larger effect may be more easily identified.

METHODS

The study included 944 adult inhabitants of the island of Korcula, as a part of larger DNA-based genetic epidemiological study in 2007. Biochemical measurements were performed in a single laboratory with stringent internal and external quality control procedures. Examinees were genotyped using Human Hap370CNV chip by Illumina, with a genome-wide scan containing 346027 single nucleotide polymorphisms (SNP).

RESULTS

A total of 31 SNPs were associated with 7 investigated traits at the level of P<1.00 x 10(-5). Nine of SNPs implicated the role of SLC2A9 in uric acid regulation (P=4.10 x 10(-6)-2.58 x 10(-12)), as previously found in other populations. All 22 remaining associations fell into the P=1.00 x 10(-5)-1.00 x 10(-6) significance range. One of them replicated the association between cholesteryl ester transfer protein (CETP) and HDL, and 7 associations were more than 100 kilobases away from the closest known gene. Nearby SNPs, rs4767631 and rs10444502, in gene kinase suppressor of ras 2 (KSR2) on chromosome 12 were associated with LDL cholesterol levels, and rs10444502 in the same gene with total cholesterol levels. Similarly, rs2839619 in gene PBX/knotted 1 homeobox 1 (PKNOX1) on chromosome 21 was associated with total and LDL cholesterol levels. The remaining 9 findings implied possible associations between phosphatidylethanolamine N-methyltransferase (PEMT) gene and total cholesterol; USP46, RAP1GDS1, and ZCCHC16 genes and triglycerides; BCAT1 and SLC14A2 genes and albumin; and NR3C2, GRIK2, and PCSK2 genes and fibrinogen.

CONCLUSION

Although this study was underpowered for most of the reported associations to reach formal threshold of genome-wide significance under the assumption of independent multiple testing, replications of previous findings and consistency of association between the identified variants and more than one studied trait make such findings interesting for further functional follow-up studies. Changed allele frequencies in isolate population may contribute to identifying variants that would not be easily identified in much larger samples in outbred populations.

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.

High differentiation among eight villages in a secluded area of Sardinia revealed by genome-wide high density SNPs analysis

To better design association studies for complex traits in isolated populations it's important to understand how history and isolation moulded the genetic features of different communities. Population isolates should not “a priori” be considered homogeneous, even if the communities are not distant and part of a small region. We studied a particular area of Sardinia called Ogliastra, characterized by the presence of several distinct villages that display different history, immigration events and population size. Cultural and geographic isolation characterized the history of these communities. We determined LD parameters in 8 villages and defined population structure through high density SNPs (about 360 K) on 360 unrelated people (45 selected samples from each village). These isolates showed differences in LD values and LD map length. Five of these villages show high LD values probably due to their reduced population size and extreme isolation. High genetic differentiation among villages was detected. Moreover population structure analysis revealed a high correlation between genetic and geographic distances. Our study indicates that history, geography and biodemography have influenced the genetic features of Ogliastra communities producing differences in LD and population structure. All these data demonstrate that we can consider each village an isolate with specific characteristics. We suggest that, in order to optimize the study design of complex traits, a thorough characterization of genetic features is useful to identify the presence of sub-populations and stratification within genetic isolates.

Historic, demographic, and genetic evidence for increased population frequencies of CCR5Delta32 mutation in Croatian Island isolates after lethal 15th century epidemics

AIM

To assess the frequency of 32 base pair deletion in CCR5 (CCR5Delta32), which has been shown to confer resistance to HIV infection in a homozygous form, in 10 isolated island communities of Dalmatia, Croatia, with different histories of exposure to epidemics during and since the medieval period.

METHODS

In 2002, DNA analysis of 100 randomly selected individuals from each of the 10 isolated communities of 5 Croatian islands (Susak, Rab, Vis, Lastovo, and Mljet) showed high levels of 3-generational endogamy, indicating limited gene flow. Five of the communities were decimated by epidemics of unknown cause between 1449-1456, while the other 5 villages remained unaffected. Genotyping of the CCR5 gene was performed using the polymerase chain reaction method with primers flanking the region containing 32-bp deletion.

RESULTS

The frequency of CCR5Delta32 in the 5 villages affected by the epidemic was 6.1-10.0%, and 1.0-3.8% in the 5 unaffected villages. The Delta32 mutation was found in 71 of 916 alleles among the individuals from the affected villages (7.5%), and in 24 of 968 alleles in unaffected villages (2.5%, chi(2)=27.3, P<10-6). A previous study in 303 random Croatian blood donors showed the frequency of the CCR5 Delta32 of 7.1% in the general population. The difference remained significant after correcting for population structure using both STRAT and STRUCTURE software and the genomic control test, to ensure results do not arise from the background genetic differences.

CONCLUSION

Our results and historical evidence, suggest that the mid-15th century epidemic could have acted as a selection pressure for the CCR5Delta32 mutation.

Is the European spatial distribution of the HIV-1-resistant CCR5-Delta32 allele formed by a breakdown of the pathocenosis due to the historical Roman expansion?

We studied the possible effects of the expansion of ancient Mediterranean civilizations during the five centuries before and after Christ on the European distribution of the mutant allele for the chemokine receptor gene CCR5 which has a 32-bp deletion (CCR5-Delta32). There is a strong evidence for the unitary origin of the CCR5-Delta32 mutation, this it is found principally in Europe and Western Asia, with generally a north-south downhill cline frequency. Homozygous carriers of this mutation show a resistance to HIV-1 infection and a slower progression towards AIDS. However, HIV has clearly emerged too recently to have been the selective force on CCR5. Our analyses showed strong negative correlations in Europe between the allele frequency and two historical parameters, i.e. the first colonization dates by the great ancient Mediterranean civilizations, and the distances from the Northern frontiers of the Roman Empire in its greatest expansion. Moreover, other studies have shown that the deletion frequencies in both German Bronze Age and Swedish Neolithic populations were similar to those found in the corresponding modern populations, and this deletion has been found in ancient DNA of around 7000 years ago, suggesting that in the past, the deletion frequency could have been relatively high in European populations. In addition, in West Nile virus pathogenesis, CCR5 plays an antimicrobial role showing that host genetic factors are highly pathogen-specific. Our results added to all these previous data suggest that the actual European allele frequency distribution might not be due to genes spreading, but to a negative selection resulting in the spread of pathogens principally during Roman expansion. Indeed, as gene flows from colonizers to European native populations were extremely low, the mutational changes might be associated with vulnerability to imported infections. To date, the nature of the parasites remains unknown; however, zoonoses could be incriminated.

Quantifying the increase in average human heterozygosity due to urbanisation

The human population is undergoing a major transition from a historical metapopulation structure of relatively isolated small communities to an outbred structure. This process is predicted to increase average individual genome-wide heterozygosity (h) and could have effects on health. We attempted to quantify this increase in mean h. We initially sampled 1001 examinees from a metapopulation of nine isolated villages on five Dalmatian islands (Croatia). Village populations had high levels of genetic differentiation, endogamy and consanguinity. We then selected 166 individuals with highly specific personal genetic histories to form six subsamples, which could be ranked a priori by their predicted level of outbreeding. The measure h was then estimated in the 166 examinees by genotyping 1184 STR/indel markers and using two different computation methods. Compared to the value of mean h in the least outbred sample, values of h in the remaining samples increased successively with predicted outbreeding by 0.023, 0.038, 0.058, 0.067 and 0.079 (P<0.0001), where these values are measured on the same scale as the inbreeding coefficient (but opposite sign). We have shown that urbanisation was associated with an average increase in h of up to 0.08-0.10 in this Croatian metapopulation, regardless of the method used. Similar levels of differentiation have been described in many populations. Therefore, changes in the level of heterozygosity across the genome of this magnitude may be common during isolate break-up in humans and could have significant health effects through the established genetic mechanism of hybrid vigour/heterosis.

Sex-specific differences of craniofacial traits in Croatia: the impact of environment in a small geographic area

BACKGROUND

Craniometric variation in humans reflects different genetic and environmental influences. Long-term climatic adaptation is less likely to show an impact on size and shape variation in a small local area than at the global level.

AIM

The aim of this work was to assess the contribution of the particular environmental factors to body height and craniofacial variability in a small geographic area of Croatia.

SUBJECTS AND METHODS

A total of 632 subjects, aged 18-21, participated in the survey. Body height, head length, head breadth, head height, head circumference, cephalic index, morphological face height, face breadth, and facial index were analysed regarding geographic, climatic and dietary conditions in different regions of the country, and correlated with the specific climatic variables (cumulative multiyear sunshine duration, cumulative multiyear average precipitation, multiyear average air temperatures) and calcium concentrations in drinking water. Significant differences between groups classified according to geographic, climatic or dietary affiliation, and the impact of the environmental predictors on the variation in the investigated traits were assessed using multiple forward stepwise regression analyses.

RESULTS

Higher body height measures in both sexes were significantly correlated with Mediterranean diet type. Mediterranean diet type also contributed to higher head length and head circumference measures in females. Cephalic index values correlated to geographic regions in both sexes, showing an increase from southern to eastern Croatia. In the same direction, head length significantly decreased in males and head breadth increased in females. Mediterranean climate was associated with higher and narrower faces in females. The analysis of the particular climatic variables did not reveal a significant influence on body height in either sex. Concurrently, climatic features influenced all craniofacial traits in females and only head length and facial index in males. Mediterranean climate, characterized by higher average sunshine duration, higher average precipitation and higher average air temperatures, was associated with longer, higher and narrower skulls, higher head circumference, lower cephalic index, and higher and narrower faces (lower facial index). Calcium concentrations in drinking water did not correlate significantly with any dependent variable.

CONCLUSION

A significant effect of environmental factors on body height and craniofacial variability was found in Croatian young adult population. This effect was more pronounced in females, revealing sex-specific craniofacial differentiation. However, the impact of environment was low and may explain only 1.0-7.32% variation of the investigated traits.

Population Substructure Can Significantly Affect Reliability of a DNA-led Process of Identification of Mass Fatality Victims

Aiming to evaluate the effects of population substructure on the reliability of a DNA correspondence in the process of human identification, we used the model of "in silico" constructed populations with and without substructure. Effects of population substructure were evaluated at the level of locus heterozygosity, Hardy-Weinberg equilibrium and mini-haplotype distribution. Inbreeding in a subpopulation of 100 individuals through 10 generations did not significantly alter the level of heterozygosity and Hardy-Weinberg equilibrium. However, analysis of mini-haplotype distribution revealed a significant homogenization in separated subpopulations. Average observed mini-haplotype frequency (f(o)) increased to threefold from expected values (f(e)), and the number of mini-haplotypes with f(o)/f(e) above 10 increased over sixfold, suggesting that the effects of population substructure on calculated likelihood ratios (LR) might be larger than previously estimated. In most criminal cases, this would not represent a problem, whereas for identifications in large-scale mass fatality events, population substructure might considerably increase the risk of false identification.

The genetic study of three population microisolates in South Tyrol (MICROS): study design and epidemiological perspectives

BACKGROUND

There is increasing evidence of the important role that small, isolated populations could play in finding genes involved in the etiology of diseases. For historical and political reasons, South Tyrol, the northern most Italian region, includes several villages of small dimensions which remained isolated over the centuries.

METHODS

The MICROS study is a population-based survey on three small, isolated villages, characterized by: old settlement; small number of founders; high endogamy rates; slow/null population expansion. During the stage-1 (2002/03) genealogical data, screening questionnaires, clinical measurements, blood and urine samples, and DNA were collected for 1175 adult volunteers. Stage-2, concerning trait diagnoses, linkage analysis and association studies, is ongoing. The selection of the traits is being driven by expert clinicians. Preliminary, descriptive statistics were obtained. Power simulations for finding linkage on a quantitative trait locus (QTL) were undertaken.

RESULTS

Starting from participants, genealogies were reconstructed for 50,037 subjects, going back to the early 1600s. Within the last five generations, subjects were clustered in one pedigree of 7049 subjects plus 178 smaller pedigrees (3 to 85 subjects each). A significant probability of familial clustering was assessed for many traits, especially among the cardiovascular, neurological and respiratory traits. Simulations showed that the MICROS pedigree has a substantial power to detect a LOD score > or = 3 when the QTL specific heritability is > or = 20%.

CONCLUSION

The MICROS study is an extensive, ongoing, two-stage survey aimed at characterizing the genetic epidemiology of Mendelian and complex diseases. Our approach, involving different scientific disciplines, is an advantageous strategy to define and to study population isolates. The isolation of the Alpine populations, together with the extensive data collected so far, make the MICROS study a powerful resource for the study of diseases in many fields of medicine. Recent successes and simulation studies give us confidence that our pedigrees can be valuable both in finding new candidates loci and to confirm existing candidate genes.

Campora: a young genetic isolate in South Italy

Genetic isolates have been successfully used in the study of complex traits, mainly because due to their features, they allow a reduction in the complexity of the genetic models underlying the trait. The aim of the present study is to describe the population of Campora, a village in the South of Italy, highlighting its properties of a genetic isolate. Both historical evidence and multi-locus genetic data (genomic and mitochondrial DNA polymorphisms) have been taken into account in the analyses. The extension of linkage disequilibrium (LD) regions has been evaluated on autosomes and on a region of the X chromosome. We defined a study sample population on the basis of the genealogy and exogamy data. We found in this population a few different mitochondrial and Y chromosome haplotypes and we ascertained that, similarly to other isolated populations, in Campora LD extends over wider region compared to large and genetically heterogeneous populations. These findings indicate a conspicuous genetic homogeneity in the genome. Finally, we found evidence for a recent population bottleneck that we propose to interpret as a demographic crisis determined by the plague of the 17th century. Overall our findings demonstrate that Campora displays the genetic characteristics of a young isolate.