Biomedical subjects

Mario Pirastu

Publications and source records attributed to Mario Pirastu.

10 recordsLinked to original sources

PubMed2006

High resolution analysis and phylogenetic network construction using complete mtDNA sequences in sardinian genetic isolates.

For mitochondrial phylogenetic analysis, the best result comes from complete sequences. We therefore decided to sequence the entire mitochondrial DNA (mtDNA) (coding and D-loop regions) of 63 individuals selected in 3 small Ogliastra villages, an isolated area of eastern Sardinia: Talana, Urzulei, and Perdasdefogu. We studied at least one individual for each of the most frequent maternal genealogical lineages belonging to haplogroups H, V, J, K, T, U, and X. We found in our 63 samples, 172 and 69 sequence changes in the coding and in the D-loop region, respectively. Thirteen out of 172 sequence changes in the coding region are novel. It is our hypothesis that some of them are characteristic of the Ogliastra region and/or Sardinia. We reconstructed the phylogenetic network of the 63 complete mtDNA sequences for the 3 villages. We also drew a network including a large number of European sequences and calculated various indices of genetic diversity in Ogliastra. It appears that these small populations remained extremely isolated and genetically differentiated compared with other European populations. We also identified in our samples a never previously described subhaplogroup, U5b3, which seems peculiar to the Ogliastra region.

DNA, Mitochondrial↗

PubMed2005

Browsing isolated population data.

BACKGROUND: In our studies of genetically isolated populations in a remote mountain area in the center of Sardinia (Italy), we found that 80-85% of the inhabitants of each village belong to a single huge pedigree with families strictly connected to each other through hundreds of loops. Moreover, intermarriages between villages join pedigrees of different villages through links that make family trees even more complicated. Unfortunately, none of the commonly used pedigree drawing tools are able to draw the complete pedigree, whereas it is commonly accepted that the visual representation of families is very important as it helps researchers in identifying clusters of inherited traits and genotypes. We had a representation issue that compels researchers to work with subsets extracted from the overall genealogy, causing a serious loss of information on familiar relationships. To visually explore such complex pedigrees, we developed PedNavigator, a browser for genealogical databases properly suited for genetic studies. RESULTS: The PedNavigator is useful for genealogical research due to its capacity to represent family relations between persons and to make a visual verification of the links during family history reconstruction. As for genetic studies, it is helpful to follow propagation of a specific set of genetic markers (haplotype), or to select people for linkage analysis, showing relations between various branch of a family tree of affected subjects. AVAILABILITY: PedNavigator is an application integrated into a Framework designed to handle data for human genetic studies based on the Oracle platform. To allow the use of PedNavigator also to people not owning the same required informatics infrastructure or systems, we developed PedNavigator Lite with mainly the same features of the integrated one, based on MySQL database server. This version is free for academic users, and it is available for download from our site http://www.shardna.com.

Algorithms↗

PubMed2004

Ocular refraction: heritability and genome-wide search for eye morphometry traits in an isolated Sardinian population.

No genes influencing oculometric phenotypes have yet been identified, despite it being well known that eye morphometry is involved in refraction and that genetics may play an important role. We have therefore performed a heritability analysis and genome-wide search (GWS) of biometric ocular traits in an isolated Sardinian population, assessing the genetic contribution and identifying the associated genetic loci. A complete eye examination including refraction and ocular biometry measurements such as axial length (AL), anterior chamber depth (ACD) and corneal curvature (CC), was performed on 789 subjects. Heritability analysis was carried out by means of parent-offspring regression and variance component models. Univariate and bivariate linkage analysis was performed by using 654 microsatellite markers spanning the genome. CC showed a mean heritability of 57%. AL and ACD were found to have significantly different variances (P<0.01) in males and females, so that heritability was calculated separately for each sex. AL had an estimated heritability in females of 31% and in males of 60%, whereas ACD had an estimated heritability of 47% in females and of 44% in males. In the GWS, the most suggestive evidence of linkage was identified on chromosome 2 for AL (LOD 2.64), on chromosome 1 for ACD (LOD 2.32) and on chromosomes 7, 2 and 3 for CC (LOD 2.50, 2.44 and 2.34, respectively). High heritability of eye morphometry traits was thus revealed. The identified loci are the first linkage signals available in ocular biometry. Notably, the observed significant differences in parental transmission deserve further study.

Adolescent↗

PubMed2004

A genomewide search using an original pairwise sampling approach for large genealogies identifies a new locus for total and low-density lipoprotein cholesterol in two genetically differentiated isolates of Sardinia.

A powerful approach to mapping the genes for complex traits is to study isolated founder populations, in which genetic heterogeneity and environmental noise are likely to be reduced and in which extended genealogical data are often available. Using graph theory, we applied an approach that involved sampling from the large number of pairwise relationships present in an extended genealogy to reconstruct sets of subpedigrees that maximize the useful information for linkage mapping while minimizing calculation burden. We investigated, through simulation, the properties of the different sets in terms of bias in identity-by-descent (IBD) estimation and power decrease under various genetic models. We applied this approach to a small isolated population from Sardinia, the village of Talana, consisting of a unique large and complex pedigree, and performed a genomewide search through variance-components linkage analysis for serum lipid levels. We identified a region of significant linkage on chromosome 2 for total serum cholesterol and low-density lipoprotein (LDL) cholesterol. Through higher-density mapping, we obtained an increased linkage for both traits on 2q21.2-q24.1, with a LOD score of 4.3 for total serum cholesterol and of 3.9 for LDL cholesterol. A replication study was performed in an independent and larger set from a genetically differentiated isolated population of the same region of Sardinia, the village of Perdasdefogu. We obtained consistent linkage to the region for total serum cholesterol (LOD score 1.4) and LDL cholesterol (LOD score 2.2), with a level of concordance uncommon for complex traits, and refined the location of the quantitative-trait locus. Interestingly, the 2q21.1-22 region has also been linked to premature coronary heart disease in Finns, and, in the adjacent 2q14 region, significant linkage with triglycerides has been reported in Hutterites.

Cholesterol↗

PubMed2004

Emergence of Talanin protein associated with human uric acid nephrolithiasis in the Hominidae lineage.

Recently, we identified a susceptibility locus for human uric acid nephrolithiasis (UAN) on 10q21-q22 and demonstrated that a novel gene (ZNF365) included in this region produces through alternative splicing several transcripts coding for four protein isoforms. Mutation analysis showed that one of them (Talanin) is associated with UAN. We examined the evolutionary conservation of ZNF365 gene through a comparative genomic approach. Searching for mouse homologs of ZNF365 transcripts, we identified a highly conserved mouse ortholog of ZNF365A transcript, expressed specifically in brain. We did not found a mouse homolog for ZNF365D transcript encoding the Talanin protein, even if we were able to identify the corresponding genomic region in mouse and rat not yet organized in canonical gene structure suggesting that ZNF365D was originated after the branching of hominoid from rodent lineage. In mouse and in most mammals, a functional uricase degrades the uric acid to allantoin, but uricase activity was lost during the Miocene epoch in hominoids. Searching for the presence of Talanin in Primates, we found a canonical intron-exon structure with several stop codons preventing protein production in Old World and New World monkeys. In humans, we observe expression and we have evidence that ZNF365D transcript produces a functional protein. It seems therefore that ZNF365D transcript emerged during primate evolution from a noncoding genomic sequence that evolved in a standard gene structure and assumed its role in parallel with the disappearance of uricase, probably against a disadvantageous excessive hyperuricemia.

Alternative Splicing↗

PubMed2003

Striking differentiation of sub-populations within a genetically homogeneous isolate (Ogliastra) in Sardinia as revealed by mtDNA analysis.

Since the reduced genetic diversity found in isolates should simplify the study of complex traits, analyses of patterns of homogeneity within populations are of particular interest. We analysed the mtDNA haplogroups and hypervariable segment I (HVS-I) sequences of 475 individuals from a geographically restricted and isolated area (Ogliastra) within Sardinia, comprehending 175 random samples from 20 out of 23 villages. The remaining 300 subjects were chosen from the other three villages, Talana, Urzulei and Perdasdefogu, by sampling all maternal lineages. A comparison with other European populations reveals that Ogliastra ranks among the most genetically homogenous population and that it has been small and isolated throughout its history. The lack of variation and the high genetic homogeneity indicate that an important founder event and a demographic expansion took place during the Neolithic (approximately 7700 years before present) in Ogliastra's mtDNA gene pool. We present highly resolved phylogenetic networks for Ogliastra and for the three sub-isolates. MtDNA differentiation in the sub-populations versus Ogliastra is revealed by a strong demarcation in their genetic pools due to distinctive founder effects and genetic drift. We found that genetic homogeneity strictly depends on a scale factor in population size and on sampling methodology. The outstanding homogeneity and the reduced female gene pool observed in Ogliastra, in the European context, hide an extremely marked differentiation in sub-isolates originated from the same archaic population. Although Ogliastra can be considered a genetically homogeneous isolate, small villages' divergent genetic histories underline the importance of more systematic analysis of DNA variation between and within populations.

DNA↗

PubMed2003

Identification of a novel gene and a common variant associated with uric acid nephrolithiasis in a Sardinian genetic isolate.

Uric acid nephrolithiasis (UAN) is a common disease with an established genetic component that presents a complex mode of inheritance. While studying an ancient founder population in Talana, a village in Sardinia, we recently identified a susceptibility locus of approximately 2.5 cM for UAN on 10q21-q22 in a relatively small sample that was carefully selected through genealogical information. To refine the critical region and to identify the susceptibility gene, we extended our analysis to severely affected subjects from the same village. We confirm the involvement of this region in UAN through identical-by-descent sharing and autozygosity mapping, and we refine the critical region to an interval of approximately 67 kb associated with UAN by linkage-disequilibrium mapping. After inspecting the genomic sequences available in public databases, we determined that a novel gene overlaps this interval. This gene is divided into 15 exons, spanning a region of approximately 300 kb and generating at least four different proteins (407, 333, 462, and 216 amino acids). Interestingly, the last isoform was completely included in the 67-kb associated interval. Computer-assisted analysis of this isoform revealed at least one membrane-spanning domain and several N- and O-glycosylation consensus sites at N-termini, suggesting that it could be an integral membrane protein. Mutational analysis shows that a coding nucleotide variant (Ala62Thr), causing a missense in exon 12, is in strong association with UAN (P=.0051). Moreover, Ala62Thr modifies predicted protein secondary structure, suggesting that it may have a role in UAN etiology. The present study underscores the value of our small, genealogically well-characterized, isolated population as a model for the identification of susceptibility genes underlying complex diseases. Indeed, using a relatively small sample of affected and unaffected subjects, we identified a candidate gene for multifactorial UAN.

Amino Acid Sequence↗

PubMed2003

Urinary glycosaminoglycans as risk factors for uric acid nephrolithiasis: case control study in a Sardinian genetic isolate.

OBJECTIVES: To assess the clinical association between glycosaminoglycan (GAG) excretion and uric acid (UA) nephrolithiasis by measuring urinary GAG levels in a case-control study conducted in a Sardinian genetic isolate. Inhibitors of crystallization such as GAGs seem to be involved in kidney stone formation. METHODS: Overnight (12-hour) urinary excretion of GAGs, calcium, oxalate, and UA were measured in urine samples from 60 patients who had formed at least one urinary stone (UA or mixed) and 52 healthy controls. The total GAG concentration was measured by a dye-binding assay, and the values were normalized against creatinine to obtain values in micrograms of GAG per milligram creatinine. Statistical analysis was performed using t tests and logistic regression analysis. RESULTS: No significant difference was found between the two groups with respect to calcium and oxalate concentrations. Nonetheless, stone formers had significantly lower levels of GAGs (29.5 +/- 2.2 versus 36.4 +/- 3.9 microg/mg creatinine, P = 0.003) and greater levels of UA (385.11 +/- 38.2 versus 298.43 +/- 31.4 mg/12 hr, P = 0.0010) than did the normal controls. CONCLUSIONS: We report that the lower excretion of GAGs in stone formers could impair their inhibitory activity on UA stone formation, and, as a consequence, it may represent a risk factor for this form of urolithiasis.

Case-Control Studies↗

PubMed2002

A new essential hypertension susceptibility locus on chromosome 2p24-p25, detected by genomewide search.

Essential hypertension (EH) is a complex disorder that results from the interaction of a number of susceptibility genes and environmental factors. We studied an isolated Sardinian village (Talana) in which the prevalence of hypertension is comparable to that in most Western populations. Talana exhibits features, such as slow demographic growth, high inbreeding, a low number of founders, stable lifestyle and culture, and accurate genealogical records, that make it suitable for the study of complex disorders. Clinical assessment of the entire adult population (N= approximately 1,000) identified approximately 100 hypertensive subjects. For our study, we selected the individuals with the most-severe EH (i.e., diastolic blood pressure >100 mm Hg), belonging to a single deep-rooted pedigree (12 generations), whose common ancestors lived in the 17th century. We performed a three-stage genomewide search using 36 affected individuals, by means of parametric linkage and allele-sharing approaches. LOD scores >1 were observed on chromosomes 1, 2, 13, 15, 17, and 19 (stage I). The most striking result was found in a 7.57-cM region on chromosome 2p24-p25. All five nonparametric linkage statistics estimated by the SimWalk2 program lie above the significance threshold of P<.008 for the whole region. Similar significance was obtained for 2p24-25 when parametric linkage (LOD score 1.99) and linkage disequilibrium mapping (P=.00006) were used, suggesting that a hypertension-susceptibility locus is located between D2S2278 and D2S168. This finding is strengthened by a recent report of linkage with marker D2S168 in a hypertensive sib-pair sample from China.

Chromosome Mapping↗

PubMed2002

Not all isolates are equal: linkage disequilibrium analysis on Xq13.3 reveals different patterns in Sardinian sub-populations.

Recent studies indicate that, whereas the Sardinian population as a whole is comparable to outbred populations for linkage disequilibrium (LD) mapping of common variants, LD in Sardinian sub-isolates is more extended, making these populations particularly suitable for this approach. To evaluate the extent of LD between microsatellite markers, we compared different sub-populations within Sardinia selected on the basis of their geographical position and isolation: two small isolated villages (Talana, Urzulei), two larger but remote areas (Ogliastra, Nuoro province) and a cohort of samples representing the wider Sardinian population. LD analysis was carried out by using six microsatellite markers that are located on Xq13.3 and that have been extensively studied in different populations. We found different extents and patterns of LD in the sub-population samples depending on their degree of isolation and demographic history. All LD measurements and haplotype analyses indicate that there is a decreasing trend from Talana (the most inbred population, LD up to 9.5-11.5 Mb) to the more outbred Sardinian population (LD only for intervals <2 Mb). In one village (Talana), five haplotype classes accounting for 80% of the entire sample perfectly matched five Ogliastra clusters, supporting the origin of the village from the Ogliastra genetic pool. In contrast, the other village (Urzulei) showed a different pattern of haplotypes with a closer relationship to the Nuoro region sub-population. LD analyses therefore show that even neighbouring isolate villages may differ in their genetic background. Here, we highlight the importance of selecting appropriate populations and/or sub-populations for the analysis of complex traits. Isolated sub-populations showing different extents of LD can provide a powerful method for mapping complex traits by LD scanning at relatively low marker density.

Chromosome Mapping↗