Shardna Life science

Pula, Italy

Shardna Life science

Pula, Italy
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Tore S.,CNR Institute of Population Genetics | Casula S.,CNR Institute of Population Genetics | Casu G.,CNR Institute of Population Genetics | Concas M.P.,CNR Institute of Population Genetics | And 11 more authors.
PLoS Genetics | Year: 2011

In contrast to large GWA studies based on thousands of individuals and large meta-analyses combining GWAS results, we analyzed a small case/control sample for uric acid nephrolithiasis. Our cohort of closely related individuals is derived from a small, genetically isolated village in Sardinia, with well-characterized genealogical data linking the extant population up to the 16th century. It is expected that the number of risk alleles involved in complex disorders is smaller in isolated founder populations than in more diverse populations, and the power to detect association with complex traits may be increased when related, homogeneous affected individuals are selected, as they are more likely to be enriched with and share specific risk variants than are unrelated, affected individuals from the general population. When related individuals are included in an association study, correlations among relatives must be accurately taken into account to ensure validity of the results. A recently proposed association method uses an empirical genotypic covariance matrix estimated from genome-screen data to allow for additional population structure and cryptic relatedness that may not be captured by the genealogical data. We apply the method to our data, and we also investigate the properties of the method, as well as other association methods, in our highly inbred population, as previous applications were to outbred samples. The more promising regions identified in our initial study in the genetic isolate were then further investigated in an independent sample collected from the Italian population. Among the loci that showed association in this study, we observed evidence of a possible involvement of the region encompassing the gene LRRC16A, already associated to serum uric acid levels in a large meta-analysis of 14 GWAS, suggesting that this locus might lead a pathway for uric acid metabolism that may be involved in gout as well as in nephrolithiasis. © 2011 Tore et al.


Sanna S.,CNR Institute of Neuroscience | Li B.,University of Michigan | Mulas A.,CNR Institute of Neuroscience | Sidore C.,CNR Institute of Neuroscience | And 27 more authors.
PLoS Genetics | Year: 2011

Complex trait genome-wide association studies (GWAS) provide an efficient strategy for evaluating large numbers of common variants in large numbers of individuals and for identifying trait-associated variants. Nevertheless, GWAS often leave much of the trait heritability unexplained. We hypothesized that some of this unexplained heritability might be due to common and rare variants that reside in GWAS identified loci but lack appropriate proxies in modern genotyping arrays. To assess this hypothesis, we re-examined 7 genes (APOE, APOC1, APOC2, SORT1, LDLR, APOB, and PCSK9) in 5 loci associated with low-density lipoprotein cholesterol (LDL-C) in multiple GWAS. For each gene, we first catalogued genetic variation by re-sequencing 256 Sardinian individuals with extreme LDL-C values. Next, we genotyped variants identified by us and by the 1000 Genomes Project (totaling 3,277 SNPs) in 5,524 volunteers. We found that in one locus (PCSK9) the GWAS signal could be explained by a previously described low-frequency variant and that in three loci (PCSK9, APOE, and LDLR) there were additional variants independently associated with LDL-C, including a novel and rare LDLR variant that seems specific to Sardinians. Overall, this more detailed assessment of SNP variation in these loci increased estimates of the heritability of LDL-C accounted for by these genes from 3.1% to 6.5%. All association signals and the heritability estimates were successfully confirmed in a sample of ~10,000 Finnish and Norwegian individuals. Our results thus suggest that focusing on variants accessible via GWAS can lead to clear underestimates of the trait heritability explained by a set of loci. Further, our results suggest that, as prelude to large-scale sequencing efforts, targeted re-sequencing efforts paired with large-scale genotyping will increase estimates of complex trait heritability explained by known loci. © 2011 Sanna et al.


Biino G.,National Research Council Italy | Casula L.,National Research Council Italy | de Terlizzi F.,IGEA S.p.A. | Adamo M.,Shardna Life science | And 10 more authors.
Bone | Year: 2010

It is now recognized that quantitative ultrasound (QUS) measures may predict osteoporotic fracture risk independently of bone mineral density. Although many studies have examined genetic and environmental components of bone mineral density and calcaneal QUS measures, few of them were addressed to phalangeal QUS phenotypes, and none to graphic trace parameters. This study aims to evaluate the relative contribution of genetics in the expression of phalangeal QUS traits in the adult healthy population of a Sardinian genetic isolate. Our sample includes 6056 men and women aged 30-103 years, from 43 extended pedigrees recruited in 10 villages of Ogliastra region in occasion of a large epidemiologic survey. Amplitude-dependent speed of sound (AD-SoS), fast wave amplitude (FWA), signal dynamic (SDy), bone transmission time (BTT) and ultrasound bone profile index (UBPI) were obtained from the non-dominant hand using the IGEA DBM Sonic Bone Profiler™. These phenotypes were first regressed on age, anthropometric and bioimpedance measures, serum calcium, phosphorus and alkaline phosphatase, alcohol and caffeine consumption, smoking status, exercise and also months since menopause and estrogens use in women. Adjusted QUS parameters were then analyzed by univariate and bivariate variance component models to obtain heritability estimates and genetic and environmental correlations. QUS parameters were correlated to age, anthropometric and bioimpedance measures, serum phosphorus, alkaline phosphatase and to reproductive history and menopause in women. All phenotypes demonstrated substantial heritabilities ranging from 0.29±0.03 for SDy to 0.55±0.03 for FWA. Proportion of variance due to all covariates ranged from 36% for SDy to 59% for BTT. Many significant genetic and environmental correlations were found between the different QUS measures. In this study, genetic factors appear to play a relevant role in determining hand QUS measures even when taking into account various important environmental factors. Furthermore, the modest genetic correlations may imply the existence of partially unique sets of genes affecting different QUS traits, thus suggesting that QUS parameters measure different properties of bone tissue. © 2009 Elsevier Inc.


Piras D.,National Research Council Italy | Doro M.G.,National Research Council Italy | Casu G.,National Research Council Italy | Melis P.M.,National Research Council Italy | And 26 more authors.
PLoS ONE | Year: 2012

Goat mtDNA haplogroup A is a poorly resolved lineage absorbing most of the overall diversity and is found in locations as distant as Eastern Asia and Southern Africa. Its phylogenetic dissection would cast light on an important portion of the spread of goat breeding. The aims of this work were 1) to provide an operational definition of meaningful mtDNA units within haplogroup A, 2) to investigate the mechanisms underlying the maintenance of diversity by considering the modes of selection operated by breeders and 3) to identify the peculiarities of Sardinian mtDNA types. We sequenced the mtDNA D-loop in a large sample of animals (1,591) which represents a non-trivial quota of the entire goat population of Sardinia. We found that Sardinia mirrors a large quota of mtDNA diversity of Western Eurasia in the number of variable sites, their mutational pattern and allele frequency. By using Bayesian analysis, a distance-based tree and a network analysis, we recognized demographically coherent groups of sequences identified by particular subsets of the variable positions. The results showed that this assignment system could be reproduced in other studies, capturing the greatest part of haplotype diversity. We identified haplotype groups overrepresented in Sardinian goats as a result of founder effects. We found that breeders maintain diversity of matrilines most likely through equalization of the reproductive potential. Moreover, the relevant amount of inter-farm mtDNA diversity found does not increase proportionally with distance. Our results illustrate the effects of breeding practices on the composition of maternal gene pool and identify mtDNA types that may be considered in projects aimed at retrieving the maternal component of the oldest breeds of Sardinia. © 2012 Piras et al.


Biino G.,National Research Council Italy | Parati G.,Sluca Hospital | Parati G.,University of Milan Bicocca | Concas M.P.,National Research Council Italy | And 4 more authors.
PLoS ONE | Year: 2013

Background and Objectives: Hypertension represents a major cause of cardiovascular morbidity and mortality worldwide but its prevalence has been shown to vary in different countries. The reasons for such differences are still matter of debate, the relative contributions given by environmental and genetic factors being still poorly defined. We estimated the current prevalence, distribution and determinants of hypertension in isolated Sardinian populations and also investigated the environmental and genetic contribution to hypertension prevalence taking advantage of the characteristics of such populations. Methods and Results: An epidemiological survey with cross-sectional design was carried out measuring blood pressure in 9845 inhabitants of 10 villages of Ogliastra region between 2002 and 2008. Regression analysis for assessing blood pressure determinants and variance component models for estimating heritability were performed. Overall 38.8% of this population had hypertension, its prevalence varying significantly by age, sex and among villages taking into account age and sex structure of their population. About 50% of hypertensives had prior cardiovascular disease. High blood pressure was independently associated with age, obesity related factors, heart rate, total cholesterol, alcohol consumption, low education and smoking status, all these factors contributing more in women than in men. Heritability was 27% for diastolic and 36% for systolic blood pressure, its contribution being significantly higher in men (57%) than in women (46%). Finally, the genetic correlation between systolic and diastolic blood pressure was 0.74, indicating incomplete pleiotropy. Conclusion: Genetic factors involved in the expression of blood pressure traits account for about 30% of the phenotypic variance, but seem to play a larger role in men; comorbidities and environmental factors remain of predominant importance, but seem to contribute much more in women. © 2013 Biino et al.


Biino G.,National Research Council Italy | Casula L.,National Research Council Italy | De Terlizzi F.,IGEA S.p.A. | Adamo M.,Shardna Life science | And 6 more authors.
American Journal of Epidemiology | Year: 2011

This study aimed at estimating the prevalence of osteoporosis and osteopenia in a Sardinian isolated population using hand quantitative ultrasound and at investigating the associated factors. The authors utilized a subset of data from a large population-based epidemiologic survey carried out in the Ogliastra region of Sardinia between 2003 and 2008. The sample consists of 6,326 men and women aged ≥30 years, who underwent quantitative ultrasound at the phalanges, bioelectrical impedance, anthropometric measurements, blood tests, and a standardized epidemiologic questionnaire collecting sociodemographic, lifestyle, medical, physiologic, and pharmacologic data. The T-score thresholds for amplitude-dependent speed of sound of-3.2 standard deviations and between-3.2 and-1 standard deviations were used to diagnose osteoporosis and osteopenia, respectively. Prevalence of osteoporosis was 17.0% in women and 5.2% in men. Logistic regression analysis revealed that factors associated with osteoporosis were age, anthropometric and bioimpedance measures, alkaline phosphatase levels, and menopause in women. High education, exercise, and beer consumption seem to be protective factors, whereas a family history of osteoporosis is a risk factor. Results show that osteoporosis in this population is comparable with that found in different countries, suggesting that quantitative ultrasound could be used more widely to detect high-risk individuals for preventing osteoporotic fractures. © 2011 The Author.


Portas L.,National Research Council Italy | Murgia F.,National Research Council Italy | Biino G.,National Research Council Italy | Concas M.P.,National Research Council Italy | And 8 more authors.
Genetics Research | Year: 2010

Isolated founder populations which exhibit great genetic and environmental homogeneity provide an attractive setting for the study of quantitative traits (QTs). Geneticists have repeatedly turned to population isolates and the past successes have prompted increased interest among medical researchers. We studied nine small isolated villages of a secluded area of Sardinia (Ogliastra), all of them characterized by a few founders, high endogamy rates, slow population expansion and a distinct genetic makeup. Anthropometric and blood parameters, 43 QTs in all, were analysed in about 9000 voluntary subjects for whom extended genealogical information was available. We explored the distribution and examined mean differences of each trait among villages by analysis of variance (ANOVA). A heritability analysis with the variance component (VC) method was performed. Results show significant differences in the distribution of most traits between groups of villages located in two distinct geographical areas already identified by a previous population structure analysis, thus supporting the existence of differentiation among sub-populations in the same region. Heritability estimates range between 30 and 89%, demonstrating that genetic effects substantially contribute to phenotypic variation of all investigated traits and that this population provides excellent research conditions for gene-mapping projects. Results suggest that history, geographic location and population structure may have influenced the genetic and phenotypic features of these isolates. Our findings may be useful for the ongoing linkage and association studies in these isolates and suggest that a thorough characterization of population is valuable to better identify genes or variants that may be rare in the population at large and peculiar to single villages. © 2010 Cambridge University Press.


Biino G.,National Research Council Italy | Balduini C.L.,University of Pavia | Casula L.,National Research Council Italy | Cavallo P.,University of Pavia | And 6 more authors.
Haematologica | Year: 2011

Background Thrombocytopenia is a common finding in several diseases but almost nothing is known about the prevalence of thrombocytopenia in the general population. We examined the prevalence of thrombocytopenia and determinants of platelet count in a healthy population with a wide age range. Design and Methods We performed a cross-sectional study on 12,517 inhabitants of ten villages (80% of residents) in a secluded area of Sardinia (Ogliastra). Participants underwent a complete blood count evaluation and a structured questionnaire, used to collect epidemiological data. Results We observed a platelet count lower than 150×109/L in 3.2% (2.8%-3.6%) of females and 4.8% (4.3%-5.4%) of males, with a value of 3.9% (3.6%-4.3%) in the entire population. Thrombocytopenia was mild (platelet count: 100×109/L -150×109L), asymptomatic and not associated with other cytopenias or overt disorders in most cases. Its standardized prevalence was quite different in different villages, with values ranging from 1.5% to 6.8%, and was negatively correlated with the prevalence of a mild form of thrombocytosis, which ranged from 0.9% to 4.5%. Analysis of platelet counts across classes of age revealed that platelet number decreased progressively with aging. As a consequence, thrombocytopenia was nearly absent in young people and its prevalence increased regularly during lifetime. The opposite occurred for thrombocytosis. Conclusions Given the high genetic differentiation among Ogliastra villages with "high" and "low" platelet counts and the substantial heritability of this quantitative trait (54%), we concluded that the propensity to present mild and transient thrombocytosis in youth and to acquire mild thrombocytopenia during aging are new genetic traits. © 2011 Ferrata Storti Foundation.

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