Prediction and visualization data for the interpretation of sarcomeric and non-sarcomeric DNA variants found in patients with hypertrophic cardiomyopathy

AbstractGenomic technologies are redefining the understanding of genotype–phenotype relationships and over the past decade, many bioinformatics algorithms have been developed to predict functional consequences of single nucleotide variants. This article presents the data from a comprehensive computational workflow adopted to assess the biomedical impact of the DNA variants resulting from the experimental study “Molecular analysis of sarcomeric and non-sarcomeric genes in patients with hypertrophic cardiomyopathy” (Bottillo et al., 2016) [1]. Several different independently methods were employed to predict the functional consequences of alleles that result in amino acid substitutions, to study the effect of some DNA variants over the splicing process and to investigate the impact of a sequence variant with respect to the evolutionary conservation

Prenatal diagnosis and post-mortem examination in a fetus with thrombocytopenia-absent radius (TAR) syndrome due to compound heterozygosity for a 1q21.1 microdeletion and a RBM8A hypomorphic allele: a case report

Background: Thrombocytopenia-absent radius syndrome is a rare autosomal recessive disorder characterized by megakaryocytic thrombocytopenia and longitudinal limb deficiencies mostly affecting the radial ray. Most patients are compound heterozygotes for a 200 kb interstitial microdeletion in 1q21.1 and a hypomorphic allele in RBM8A, mapping in the deleted segment. At the moment, the complete molecular characterization of thrombocytopenia-absent radius syndrome is limited to a handful of patients mostly ascertained in the pediatric age. Case presentation. We report on a fetus with bilateral upper limb deficiency found at standard prenatal ultrasound examination. The fetus had bilateral radial agenesis and humeral hypo/aplasia with intact thumbs, micrognathia and urinary anomalies, indicating thrombocytopenia-absent radius syndrome. Molecular studies demonstrated compound heterozygosity for the 1q21.1 microdeletion and the RBM8A rs139428292 variant at the hemizygous state, inherited from the mother and father, respectively. Conclusion: The molecular information allowed prenatal diagnosis in the following pregnancy resulting in the birth of a healthy carrier female. A review was carried out with the attempt to the trace the fetal ultrasound presentation of thrombocytopenia-absent radius syndrome and discussing opportunities for second-tier molecular studies within a multidisciplinary setting. © 2013 Bottillo et al.; licensee BioMed Central Ltd

Late diagnosis of lateral meningocele syndrome in a 55-year-old woman with symptoms of joint instability and chronic musculoskeletal pain

Lateral meningocele syndrome (LMS) is a rare hereditary connective tissue disorder characterized by pan-spinal meningoceles, specific facial dysmorphism, skeletal and soft tissue abnormalities, and hypotonia and/or muscle weakness. LMS has been observed in eleven patients with two instances of vertical transmission, and seven sporadic cases with an age at diagnosis ranging from 25 months to 33 years. We report on a further observation of LMS in a 55-year-old woman presenting with a long history of joint instability, chronic musculoskeletal pain, and iatrogenic bladder and anorectal dysfunction due to irreversible nerve damage after surgical excision of a meningeal cyst. Her clinical characteristics are compared with those of previously reported patients, as well as two further cases originally diagnosed with Hajdu-Cheney and Ehlers-Danlos syndromes, but displaying typical features of LMS. © 2013 Wiley Periodicals, Inc.Lateral meningocele syndrome (LMS) is a rare hereditary connective tissue disorder characterized by pan-spinal meningoceles, specific facial dysmorphism, skeletal and soft tissue abnormalities, and hypotonia and/or muscle weakness. LMS has been observed in eleven patients with two instances of vertical transmission, and seven sporadic cases with an age at diagnosis ranging from 25 months to 33 years. We report on a further observation of LMS in a 55-year-old woman presenting with a long history of joint instability, chronic musculoskeletal pain, and iatrogenic bladder and anorectal dysfunction due to irreversible nerve damage after surgical excision of a meningeal cyst. Her clinical characteristics are compared with those of previously reported patients, as well as two further cases originally diagnosed with Hajdu–Cheney and Ehlers–Danlos syndromes, but displaying typical features of LMS

TFR2-related hereditary hemochromatosis as a frequent cause of primary iron overload in patients from Central-Southern Italy

Objective: Hereditary hemochromatosis (HH) is a common Mendelian disorder of iron metabolism. Eighty percent of northern Europeans descendant HH patients carry the same mutation (p.C282Y) in the HFE gene. Simultaneously, due to a founder effect, its frequency varies considerably between different populations. In Central-Southern Italy the prevalence of p.C282Y mutation is low and in several patients the disease has different causes. Four additional rarer forms have been described. Type 3 HH has been reported in about 50 families and no more than 30 TFR2 pathogenic mutations have been globally identified. The aim of this study is to assess the TFR2 role in non-HFE HH pathogenesis. Study design and setting: TFR2 sequence analysis was performed on 45 Italian patients without HFE mutations. Results: This study revealed TFR2 biallelic pathogenic mutations in 7/45 (15.6%) individuals. Moreover monoallelic TFR2 deleterious defects (18%) or polymorphisms with unclear meaning (36%) were identified. Besides, we recognized 10 novel variants and 9 described changes. Conclusion: We believe this to be the largest series of type 3 HH patients described so far. Present findings support the hypothesis of a main role of the TFR2 gene in HH pathogenesis in those regions, such as Central-Southern Italy, where the p.C282Y frequency is low. (C) 2013 Elsevier Inc. All rights reserved.Objective: Hereditary hemochromatosis (HH) is a common mendelian disorder of iron metabolism. Eighty percent of northern Europeans descendant HH patients carry the same mutation (p.C282Y) in HFE gene. Simultaneously, due to a founder effect, its frequency varies considerably between different populations. In Central-Southern Italy the prevalence of p.C282Y mutation is low and in several patients the disease has different causes. Four additional rarer forms have been described. Type 3 HH has been reported in about 50 families and no more than 30 TFR2 pathogenic mutations have been globally identified. The aim of this study is to assess the TFR2 role in non-HFE HH pathogenesis. Study Design and Setting: TFR2 sequence analysis was performed on 45 Italian patients without HFE mutations. Results: This study revealed TFR2 biallelic pathogenic mutations in 7/45 (15,6%) individuals. Moreover monoallelic TFR2 deleterious defects (18%) or polymorphisms with unclear meaning (36%) were identified. Besides, we recognised 10 novel variants and 9 described changes. Conclusion: This is supposedly the largest series of type 3 HH patients described so far. Present findings support the hypothesis of a main role of the TFR2 gene in HH pathogenesis in those regions, such as Central-Southern Italy, where the p.C282Y frequency is low

Identification of a novel duplication in the APC gene using multiple ligation probe amplification in a patient with familial adenomatous polyposis

Germline mutations in the adenomatous polyposis coli (APC) gene cause familial adenomatous polyposis (FAP), an autosomal dominant disease characterized by hundreds to thousands of adenomatous polyps in the colon and rectum, with progression to colorectal cancer. The majority of APC mutations are nucleotide substitutions and frameshift mutations that result in truncated proteins. Recently, large genomic alterations of the APC gene have been reported in EAR DNA from 15 FAP patients, in whom no APC germline mutations were detected with denaturing high performance liquid chromatography, was analyzed with multiplex ligation-dependent probe amplification (MLPA) to evaluate gross genomic alterations in the APC gene. In one case, MLPA identified a novel duplication of exons 2-6 in one copy of the APC gene. Reverse transcriptase-polymerase chain reaction revealed that the mutant allele contained an in-frame multiexon duplication including 18 nucleotides located in exon 2, upstream of the ATG initiation codon. The presence of a premature stop codon in the duplicated sequence leads to the synthesis of a truncated APC polypeptide. These findings highlight the utility of evaluating infrequent APC mutation events in RAP patients using MLPA. (C) 2008 Elsevier Inc. All rights reserved

Clinical features predicting identification of CDKN2A mutations in Italian patients with familial cutaneous melanoma

CDKN2A is the most common, most penetrant gene whom germline mutations predisposing to cutaneous familial melanoma (FAM). Multiple primary melanoma (MPM), early age at onset, >2 affected members and pancreatic cancer are consistent features predicting positive test. However, the impact that cumulative clinical features have on the likelihood of molecular testing is unknown. In this work, genotype-phenotype correlations focused on selected clinical features were performed in 100 Italian FAM unrelated patients. Molecular studies of CDKN2A mutations were performed by direct sequencing. Statistical study included multiple correspondence analysis, uni- and multivariate analyses, and individual patient's probability calculation. MPM, >2 affected family members, Breslow thickness >0.4 mm, and age at onset <= 41 years were the unique independent features predicting positive CDKN2A screening. The rate of positive testing ranged from 93.2% in the presence of all of them, to 0.4% in their absence. The contribution of each of them was quantified accordingly, with MPM being the most significant. These findings confirm previous data and add novel insights for the role of accurate patients' selection in CDKN2A screening. (C) 2011 Elsevier Ltd. All rights reserved

Association of hepcidin promoter c.-582 A>G variant and iron overload in thalassemia major

The liver peptide hepcidin is the key regulator of iron homeostasis. This report shows that liver iron content and serum ferritin levels are greater in thalassemia patients with the −582G polymorphic change in the hepcidin promoter as compared with patients with the wild-type (A) sequence. This observation suggests that this change might influence the iron status of irregularly chelated thalassemic patients. See related perspective article on page 1185

Prediction and visualization data for the interpretation of sarcomeric and non-sarcomeric DNA variants found in patients with hypertrophic cardiomyopathy

Genomic technologies are redefining the understanding of geno-type–phenotype relationships and over the past decade, manybioinformatics algorithms have been developed to predict func-tional consequences of single nucleotide variants. This articlepresents the data from a comprehensive computational workflowadopted to assess the biomedical impact of the DNA variantsresulting from the experimental study“Molecular analysis of sar-comeric and non-sarcomeric genes in patients with hypertrophiccardiomyopathy”(Bottillo et al., 2016)[1]. Several different inde-pendently methods were employed to predict the functionalconsequences of alleles that result in amino acid substitutions, tostudy the effect of some DNA variants over the splicing process and o investigate the impact of a sequence variant with respect to theevolutionary conservation

AXIN2 germline mutations are rare in familial melanoma

[No abstract available