@article {10532, title = {LTF and DEFB1 polymorphisms are associated with susceptibility toward chronic periodontitis development.}, journal = {Oral Dis}, volume = {23}, year = {2017}, month = {2017 Oct}, pages = {1001-1008}, abstract = {

OBJECTIVES: Chronic periodontitis is a common pathological condition that affects the supporting tissue of the teeth, leading to progressive alveolar bone destruction and teeth loss. The disease is caused by bacteria and derives from an altered host immune and inflammatory response, also involving different factors such as the oral hygiene, smoking, and genetic background. The innate immune response, the first line of host defense, could also play an important role in the susceptibility to chronic periodontitis. In this study, we evaluated the possible association between periodontal disease and seven genetic variations within DEFB1 and LTF genes, encoding for β-defensins 1 and lactoferrin (two members of oral innate immune system), in an Italian isolated population.

SUBJECTS AND METHODS: DEFB1 5{\textquoteright}UTR g. -52G>A (rs1799946), g. -44C>G (rs1800972), g. -20G>A (rs11362), 3{\textquoteright}UTR c*5G>A (rs1047031), c*87A>G (rs1800971), LTF p.Ala29Thr (rs1126477), and p.Lys47Arg (rs1126478) single nucleotide polymorphisms (SNPs) were analyzed in 155 healthy individuals and 439 chronic periodontitis patients from North-East Italy.

RESULTS: Significant associations were found between periodontitis and g. -20G>A (rs11362) and g. -44C>G (rs1800972) SNPs in DEFB1 gene as well as p.Ala29Thr (rs1126477) and p.Lys47Arg (rs1126478) SNPs in LTF gene.

DISCUSSION: Our results suggest the involvement of DEFB1 and LTF genetic variations in the susceptibility toward development of periodontitis.

}, keywords = {Adolescent, Adult, Aged, Aged, 80 and over, beta-Defensins, Case-Control Studies, Chronic Periodontitis, Female, Genetic Predisposition to Disease, Humans, Lactoferrin, Male, Middle Aged, Polymorphism, Single Nucleotide, Young Adult}, issn = {1601-0825}, doi = {10.1111/odi.12689}, author = {Zupin, L and Robino, A and Navarra, C O and Pirastu, N and Di Lenarda, R and Gasparini, P and Crovella, S and Bevilacqua, L} } @article {7782, title = {MultiMeta: an R package for meta-analyzing multi-phenotype genome-wide association studies.}, journal = {Bioinformatics}, volume = {31}, year = {2015}, month = {2015 Aug 15}, pages = {2754-6}, abstract = {

UNLABELLED: As new methods for multivariate analysis of genome wide association studies become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance-based method for meta-analysis, generalized to an n-dimensional setting.

AVAILABILITY AND IMPLEMENTATION: The R package MultiMeta can be downloaded from CRAN.

CONTACT: dragana.vuckovic@burlo.trieste.it; vi1@sanger.ac.uk

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

}, issn = {1367-4811}, doi = {10.1093/bioinformatics/btv222}, author = {Vuckovic, D and Gasparini, P and Soranzo, N and Iotchkova, V} } @article {3513, title = {Hereditary hearing loss: a 96 gene targeted sequencing protocol reveals novel alleles in a series of Italian and Qatari patients.}, journal = {Gene}, volume = {542}, year = {2014}, month = {2014 Jun 1}, pages = {209-16}, abstract = {

Deafness is a really common disorder in humans. It can begin at any age with any degree of severity. Hereditary hearing loss is characterized by a vast genetic heterogeneity with more than 140 loci described in humans but only 65 genes so far identified. Families affected by hearing impairment would have real advantages from an early molecular diagnosis that is of primary relevance in genetic counseling. In this perspective, here we report a family-based approach employing Ion Torrent DNA sequencing technology to analyze coding and UTR regions of 96 genes related to hearing function and loss in a first series of 12 families coming from Italy and Qatar. Using this approach we were able to find the causative gene in 4 out of these 12 families (33\%). In particular 5 novel alleles were identified in the following genes LOXHD1, TMPRSS3, TECTA and MYO15A already associated with hearing impairment. Our study confirms the usefulness of a targeted sequencing approach despite larger numbers are required for further validation and for defining a molecular epidemiology picture of hearing loss in these two countries.

}, keywords = {Alleles, Amino Acid Sequence, Carrier Proteins, Extracellular Matrix Proteins, Female, Genetic Testing, GPI-Linked Proteins, Hearing Loss, Humans, Italy, Male, Membrane Proteins, Molecular Sequence Data, Mutation, Myosins, Neoplasm Proteins, Pedigree, Qatar, Sequence Analysis, DNA, Serine Endopeptidases, Untranslated Regions}, issn = {1879-0038}, doi = {10.1016/j.gene.2014.03.033}, author = {Vozzi, D and Morgan, A and Vuckovic, D and D{\textquoteright}Eustacchio, A and Abdulhadi, K and Rubinato, E and Badii, R and Gasparini, P and Girotto, G} } @article {1804, title = {De novo 911 Kb interstitial deletion on chromosome 1q43 in a boy with mental retardation and short stature.}, journal = {Eur J Med Genet}, volume = {55}, year = {2012}, month = {2012 Feb}, pages = {117-9}, abstract = {

Patients with distal deletions of chromosome 1q have a recognizable syndrome that includes microcephaly, hypoplasia or agenesis of the corpus callosum, and psychomotor retardation. Although these symptoms have been attributed to deletions of 1q42-1q44, the minimal chromosomal region involved has not yet defined. In this report, we describe a 7 years old male with mental retardation, cryptorchid testes, short stature and alopecia carrying only an interstitial de novo deletion of 911 Kb in the 1q43 region (239,597,095-240,508,817) encompassing three genes CHRM3, RPS7P5 and FMN2.

}, keywords = {Child, Chromosomes, Human, Pair 1, Dwarfism, Humans, Intellectual Disability, Male, Sequence Deletion}, issn = {1878-0849}, doi = {10.1016/j.ejmg.2011.11.004}, author = {Perrone, M D and Rocca, M S and Bruno, I and Faletra, F and Pecile, V and Gasparini, P} } @article {1954, title = {Identification of a New Mutation (L46P) in the Human NOG Gene in an Italian Patient with Symphalangism Syndrome.}, journal = {Mol Syndromol}, volume = {3}, year = {2012}, month = {2012 Jun}, pages = {21-24}, abstract = {

Proximal symphalangism (SYM1) is a joint morphogenesis disorder characterized by stapes ankylosis, proximal interphalangeal joint fusion, skeletal anomalies and conductive hearing loss. Noggin is a bone morphogenetic protein (BMP) antagonist essential for normal bone and joint development in humans and mice. Autosomal dominant mutations have been described in the NOG gene, encoding the noggin protein. We analyzed an Italian sporadic patient with SYM1 due to a novel NOG mutation (L46P) based on a c.137T>C transition. A different pathogenic mutation in the same codon (L46D) has been previously described in an in vivo chicken model. An in silico model shows a decreased binding affinity between noggin and BMP7 for both L46D and L46P compared to the wild type. Therefore, this codon should play an important role in BMP7 binding activity of the noggin protein and consequently to the joint morphogenesis.

}, issn = {1661-8769}, doi = {000337928}, author = {Athanasakis, E and Biarn{\'e}s, X and Bonati, M T and Gasparini, P and Faletra, F} } @article {1988, title = {Phylloid pattern of hypomelanosis closely related to chromosomal abnormalities in the 13q detected by SNP array analysis.}, journal = {Dermatology}, volume = {225}, year = {2012}, month = {2012}, pages = {294-7}, abstract = {

Phylloid hypomelanosis is a distinct type of pigmentary mosaicism characterized by congenital hypochromic macules resembling a floral ornament with various elements such as round or oval patches, asymmetrical macules similar to begonia leaves, or oblong lesions. It has been found to be predominantly associated with abnormalities in chromosome 13 and sometimes as-sociated with different extracutaneous abnormalities. Here, we report 2 new cases of phylloid hypomelanosis due to mosaicism involving chromosome 13. The first one is a mosaicism for a supernumerary marker belonging to chromosome 13 and the second one is the first report of phylloid hypomelanosis associated with a mosaic deletion of 13q. Because of the extremely low level of mosaicism in these 2 cases, SNP array analysis on skin fibroblasts was carried out, showing a 13q21.33-q34 duplication (71,024,411-115,103,529) and a 13q13.3-q34 (38,368,012-115,103,529) deletion. Both cases underline on the one hand the strict connection between phylloid hypomelanosis and anomalies of chromosome 13, and on the other hand the relevance of the SNP array analysis on skin fibroblasts in the detection of low-level mosaicism.

}, keywords = {Chromosomes, Human, Pair 13, Humans, Hypopigmentation, Male, Mosaicism, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide}, issn = {1421-9832}, doi = {10.1159/000342884}, author = {Faletra, F and Berti, I and Tommasini, A and Pecile, V and Cleva, L and Alberini, E and Bruno, I and Gasparini, P} } @article {1953, title = {Two Novel COH1 Mutations in an Italian Patient with Cohen Syndrome.}, journal = {Mol Syndromol}, volume = {3}, year = {2012}, month = {2012 Jun}, pages = {30-33}, abstract = {

Cohen syndrome (CS) is an autosomal recessive disease caused by mutations in the COH1 gene. It is characterized by intellectual disability, hypotonia, joint hyperlaxity, severe myopia, characteristic facial dysmorphisms and, in some cases, intermittent isolated neutropenia. We investigated an Italian patient with CS together with his family. Genetic analysis disclosed 2 novel mutations: the first is an intronic mutation (c.8697-9A>G) creating a new splice site 8 nucleotides upstream, and the second is a duplication of 1 base (c.10156dupA) generating a premature stop codon. The compound heterozygous mutations explain the proband{\textquoteright}s phenotype and improved the knowledge of genotype-phenotype correlation.

}, issn = {1661-8769}, doi = {000338816}, author = {Athanasakis, E and Fabretto, A and Faletra, F and Mocenigo, M and Morgan, A and Gasparini, P} }