Publications by authors named "Benedetto Pennato"

4 Publications

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[Heart without HDL.Tangier disease].

Recenti Prog Med 2009 Apr;100(4):180-3

Scuola Superiore Sant'Anna, Pisa.

A 37-year-old man was referred to our lipid clinic because of profound plasma lipid alteration. He presented large and orange tonsils, hepatosplenomegaly. No corneal opacities or other ocular abnormalities as well as no nervous system abnormalities were evident. Haematologic alterations included thrombocytopenia and stomatocytes. HDL and apolipoprotein A-I concentrations were 4 and 3.9 mg/dL, respectively. Because of a severe coronary atherosclerosis documented by coronary angiography, he underwent percutaneous revascularization. Nine months later, he experienced restenosis of the proximal anterior descending coronary artery and was referred for CABG. The patient was diagnosed with Tangier disease on the basis of the pathognomonic triad of the disease: HDL deficiency, low plasma cholesterol concentration accompanied by normal (or even elevated) triglyceride levels and hyperplastic orange tonsils.
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April 2009

Haplotypic structure of the X chromosome in the COGA population sample and the quality of its reconstruction by extant software packages.

BMC Genet 2005 Dec 30;6 Suppl 1:S77. Epub 2005 Dec 30.

Center of Statistical Genetics, c/o Centro Retrovirus, SS Abetone e Brennero 2, 56127 Pisa, Italy.

Background: The haplotypes of the X chromosome are accessible to direct count in males, whereas the diplotypes of the females may be inferred knowing the haplotype of their sons or fathers. Here, we investigated: 1) the possible large-scale haplotypic structure of the X chromosome in a Caucasian population sample, given the single-nucleotide polymorphism (SNP) maps and genotypes provided by Illumina and Affimetrix for Genetic Analysis Workshop 14, and, 2) the performances of widely used programs in reconstructing haplotypes from population genotypic data, given their known distribution in a sample of unrelated individuals.

Results: All possible unrelated mother-son pairs of Caucasian ancestry (N = 104) were selected from the 143 families of the Collaborative Study on the Genetics of Alcoholism pedigree files, and the diplotypes of the mothers were inferred from the X chromosomes of their sons. The marker set included 313 SNPs at an average density of 0.47 Mb. Linkage disequilibrium between pairs of markers was computed by the parameter D', whereas for measuring multilocus disequilibrium, we developed here an index called D*, and applied it to all possible sliding windows of 5 markers each. Results showed a complex pattern of haplotypic structure, with regions of low linkage disequilibrium separated by regions of high values of D*. The following programs were evaluated for their accuracy in inferring population haplotype frequencies: 1) ARLEQUIN 2.001; 2) PHASE 2.1.1; 3) SNPHAP 1.1; 4) HAPLOBLOCK 1.2; 5) HAPLOTYPER 1.0. Performances were evaluated by Pearson correlation (r) coefficient between the true and the inferred distribution of haplotype frequencies.

Conclusion: The SNP haplotypic structure of the X chromosome is complex, with regions of high haplotype conservation interspersed among regions of higher haplotype diversity. All the tested programs were accurate (r = 1) in reconstructing the distribution of haplotype frequencies in case of high D* values. However, only the program PHASE realized a high correlation coefficient (r > 0.7) in conditions of low linkage disequilibrium.
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December 2005

Validation of a large Italian Database of 15 STR loci.

Forensic Sci Int 2006 Jan 22;156(2-3):266-8. Epub 2005 Apr 22.

Center of Statistical Genetics, SS Abetone e Brennero 2, 56127 Pisa, Italy.

Results from a collaborative exercise with proficiency testing conducted by 20 Italian laboratories on the 15 loci included in the Identifiler kit were analyzed by allele sharing methods and by standard population genetics tests. The validated database, including about 1500 subjects, was merged with that of a previous exercise conducted on nine loci, and the resulting allele frequencies, subdivided by Italian region, were published on-line.
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January 2006