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Background Targeted resequencing has become the most used and cost-effective approach for identifying causative mutations of Mendelian diseases both for diagnostics and research purposes. Due to very rapid technological progress, NGS laboratories are expanding their capabilities to address the increasing number of analyses. Several open source tools are available to build a generic variant calling pipeline, but a tool able to simultaneously execute multiple analyses, organize, and categorize the samples is still missing. Results Here we describe VarGenius, a Linux based command line software able to execute customizable pipelines for the analysis of multiple targeted resequencing data using parallel computing. VarGenius provides a database to store the output of the analysis (calling quality statistics, variant annotations, internal allelic variant frequencies) and sample information (personal data, genotypes, phenotypes). VarGenius can also perform the “joint analysis” of hundreds of samples with a single command, drastically reducing the time for the configuration and execution of the analysis. VarGenius executes the standard pipeline of the Genome Analysis Tool-Kit (GATK) best practices (GBP) for germinal variant calling, annotates the variants using Annovar, and generates a user-friendly output displaying the results through a web page. VarGenius has been tested on a parallel computing cluster with 52 machines with 120GB of RAM each. Under this configuration, a 50 M whole exome sequencing (WES) analysis for a family was executed in about 7 h (trio or quartet); a joint analysis of 30 WES in about 24 h and the parallel analysis of 34 single samples from a 1 M panel in about 2 h. Conclusions We developed VarGenius, a “master” tool that faces the increasing demand of heterogeneous NGS analyses and allows maximum flexibility for downstream analyses. It paves the way to a different kind of analysis, centered on cohorts rather than on singleton. Patient and variant information are stored into the database and any output file can be accessed programmatically. VarGenius can be used for routine analyses by biomedical researchers with basic Linux skills providing additional flexibility for computational biologists to develop their own algorithms for the comparison and analysis of data. The software is freely available at: https://github.com/frankMusacchia/VarGenius

The peculiar photoluminescence characteristics of radiation-induced colour centres in lithium fluoride (LiF), well known for applications in optically-pumped tuneable lasers and broad-band miniaturised light-emitting photonic devices operating at room-temperature, are under exploitation in passive imaging detectors and dosimeters based on visible radiophotoluminescence in LiF crystals and polycrystalline thin films. Their high intrinsic spatial resolution, wide dynamic range and large field of view, combined with easy handling, ambient-light operation and no development need, allow to successfully extend their use from X-ray imaging to proton-beam advanced diagnostics and dosimetry, even at those low dose values that are typical of hadrontherapy. After exposure, the latent images stored in LiF as local formations of F 2 and F 3 + aggregate defects are read with an optical fluorescence microscope under illumination in the blue spectral range. Their visible emission intensity was found to be linearly proportional to the dose over at least three orders of magnitude, so that bi-dimensional LiF solid-state dosimeters based on spectrally-integrated radiophotoluminescence reading can be envisaged. Taking advantage of the low thickness of LiF thin films, transversal proton beam dose mapping was demonstrated at low proton energies, even at high doses. Recent results and advances concerning LiF crystals and polycrystalline thin film characterisation in the linearity range are presented and discussed with the aim of highlighting challenges related to increasing the LiF film detector radiation sensitivity to both particles (protons) and photons (X-rays), although therapeutic dose values typical of clinical radiotherapy are still a big challenge.

Thermal neutron detection plays a crucial role in numerous scientific and technical applications such as nuclear reactor physics, particle accelerators, radiotherapy, materials analysis and space exploration. There are several challenges associated with the accurate identification and quantification of thermal neutrons. The present work proposes a detailed characterization of a Timepix3 (TPX3) detector equipped with a Lithium Fluoride ( 6 LiF) converter in order to study its response to thermal neutrons that are identified through the 6 Li(n, α ) 3 H reaction. The TPX3-based test system has been installed at the HOTNES facility in ENEA and the analysis highlighted its excellent performance showing high effectiveness in the identification of neutrons through morphological analysis of tracks produced by alpha and triton particles, after accurate discrimination from the gamma background. With the use of Monte Carlo simulations, it has been demonstrated that the main contribution is due to tritons and its signal can be used effectively in the identification of thermal neutrons obtaining an efficiency of 0.9 % for 25 meV neutrons. This allows the TPX3 to have important applications as an environmental monitor for thermal neutrons. This monitoring system can be simply realized and is easy to manage because of its compact size and its digital acquisition that allows a real-time analysis.

Background Myosin heavy chain 7 ( MYH7 )-related myopathies are emerging as an important group of muscle diseases of childhood and adulthood, with variable clinical and histopathological expression depending on the type and location of the mutation. Mutations in the head and neck domains are a well-established cause of hypertrophic cardiomyopathy whereas mutation in the distal regions have been associated with a range of skeletal myopathies with or without cardiac involvement, including Laing distal myopathy and Myosin storage myopathy. Recently the spectrum of clinical phenotypes associated with mutations in MYH7 has increased, blurring this scheme and adding further phenotypes to the list. A broader disease spectrum could lead to misdiagnosis of different congenital myopathies, neurogenic atrophy and other neuromuscular conditions. Results As a result of a multicenter Italian study we collected clinical, histopathological and imaging data from a population of 21 cases from 15 families, carrying reported or novel mutations in MYH7 . Patients displayed a variable phenotype including atypical pictures, as dropped head and bent spine, which cannot be classified in previously described groups. Half of the patients showed congenital or early infantile weakness with predominant distal weakness. Conversely, patients with later onset present prevalent proximal weakness. Seven patients were also affected by cardiomyopathy mostly in the form of non-compacted left ventricle. Muscle biopsy was consistent with minicores myopathy in numerous cases. Muscle MRI was meaningful in delineating a shared pattern of selective involvement of tibialis anterior muscles, with relative sparing of quadriceps. Conclusion This work adds to the genotype-phenotype correlation of MYH7 -relatedmyopathies confirming the complexity of the disorder.

Mutations in the fukutin-related protein (FKRP) have recently been demonstrated to cause limb girdle muscular dystrophy type 2I (LGMD2I), one of the most common forms of the autosomal recessive LGMDs in Europe. We performed a systematic clinical and muscle MRI assessment in 6 LGMD2I patients and compared these findings with those of 14 patients with genetically confirmed diagnosis of other forms of autosomal recessive LGMDs or dystrophinopathies. All LGMD2I patients had a characteristic clinical phenotype with predominant weakness of hip flexion and adduction, knee flexion and ankle dorsiflexion. These findings were also mirrored on MRI of the lower extremities which demonstrated marked signal changes in the adductor muscles, the posterior thigh and posterior calf muscles. This characteristic clinical and MRI phenotype was also seen in LGMD2A. However, in LGMD2A there was a selective involvement of the medial gastrocnemius and soleus muscle in the lower legs which was not seen in LGMD2I. The pattern in LGMD2A and LGMD2I were clearly different from the one seen in alpha-sarcoglycanopathy and dystrophinopathy type Becker which showed marked signal abnormalities in the anterior thigh muscles. Our results indicate that muscular MRI is a powerful tool for differentiating LGMD2I from other forms of autosomal recessive LGMDs and dystrophinopathies.

Limb girdle muscular dystrophy (LGMD) type 2A (LGMD2A) is caused by mutations in the CAPN3 gene encoding for calpain‐3, a muscle specific protease. While a large number of CAPN3 gene mutations have already been described in calpainopathy patients, the diagnosis has recently shifted from molecular genetics towards biochemical assay of defective protein. However, an estimate of sensitivity and specificity of protein analysis remains to be established. Thus, we first correlated protein and molecular data in our large LGMD2A patient population. By a preliminary immunoblot screening for calpain‐3 protein of 548 unclassified patients with various phenotypes (LGMD, myopathy, or elevated levels of serum creatine kinase [hyperCKemia]), we selected 208 cases for CAPN3 gene mutation analysis: 69 had protein deficiency and 139 had normal expression. Mutation search was conducted using SSCP, denaturing high performance liquid chromatography (DHPLC), amplification refractory mutation system (ARMS‐PCR), and direct sequencing methods. We identified 58 LGMD2A mutant patients: 46 (80%) had a variable degree of protein deficiency and 12 (20%) had normal amount of calpain‐3. We calculated that the probability of having LGMD2A is very high (84%) when patients show a complete calpain‐3 deficiency and progressively decreases with the amount of protein; this new data offers an important tool for genetic counseling when only protein data are available. A total of 37 different CAPN3 gene mutations were detected, 10 of which are novel. In our population, 87% of mutant alleles were concentrated in seven exons (exons 1, 4, 5, 8, 10, 11, and 21) and 61% correspond to only eight mutations, indicating the regions where future molecular analysis could be restricted. This study reports the largest collection of LGMD2A patients so far in which both protein and gene mutations were obtained to draw genotype–protein–phenotype correlations and provide insights into a critical protein domain. Hum Mutat 24:52–62, 2004. © 2004 Wiley‐Liss, Inc.

Background: Melanocortin-4 receptor (MC4R) mutations have been reported as the most common single genetic cause of obesity in some populations and it has been suggested that they may be responsible for more than 4% of early-onset obesity. Objectives: To verify the presence of mutations of the MC4R coding region in children from southern Italy with early-onset obesity. Subjects and Methods: Two-hundred and eight unrelated obese children and adolescents were included in the study. The average age at obesity onset was 4.5±2.6 y. MC4R coding region was screened using both single-strand conformation polymorphism (SSCP) analysis and denaturing high-performance liquid chromatography (DHPLC). Automatic sequencing of PCR products of all individuals that showed an aberrant SSCP and/or DHPLC pattern was performed. Results: One novel missense mutation and one previously described polymorphism (Vall03Ile) were identified. The missense mutation C142T, resulting in the substitution of proline with serine at codon 48, within the first MC4R transmembrane domain, was detected at the heterozygous state in a 15-y-old obese girl (body mass index (BMI)=35 kg/m2) who has been obese since she was 8 y old. The mutation co-segregated with the obesity phenotype for over three generations and was not found in the control population. Conclusions: Our data show MC4R obesity causing mutations in less than 0.5% of the patients (ie 1 out of 208 patients) and therefore indicate a low prevalence of MC4R variants in the obese population from southern Italy. The specific genetic background of the Mediterranean population could make it difficult for MC4R mutations to produce an essentially polygenic trait such as common obesity, at least during childhood.

Optically transparent lithium fluoride (LiF) thin films, thermally evaporated on Si(100) substrates, are under investigation as novel radiation detectors based on radiophotoluminescence for imaging of the full Bragg curves of proton beams produced by a linear accelerator for proton therapy under development at ENEA C.R. Frascati. Proton irradiation induces the formation of stable colour centres in LiF, amongst which the broadband light-emitting F 2 and F 3 + aggregate defects, whose concentrations are locally proportional to the energy deposited in the material. Their spatial distributions in the irradiated LiF thin films and crystals are carefully measured by acquiring the latent two-dimensional visible fluorescence images with an optical microscope under blue lamp excitation. Several LiF films grown on silicon substrate were irradiated in air at increasing proton energies up to 35 MeV with their surface parallel to the particle beam and a cleaved edge perpendicularly facing it; for each sample, the fluorescence image acquired from the top surface side of the film allows to obtain the depth profile of the energy released by protons. Differences in colour centre distributions detected in LiF films with respect to LiF crystals are presented and discussed. Accurate Monte Carlo simulations allow to fully explain their experimental behaviours, paving the way towards using LiF film radiation detectors on silicon for the advanced diagnostics of proton beams at typical particle energies used for proton therapy.

Limb girdle muscular dystrophy 2A (LGMD2A), caused by calpain 3 deficiency, is currently diagnosed through the immunodetection of muscle protein by Western blot (WB) analysis . However, WB may provide normal results in patients with LGMD2A. The case of a female (3y 6mo of age) is described. She was found to be affected by asymptomatic hypercreatine-kinaesaemia during routine biochemical analysis at 10 months of age and had developed myopathic signs at the last neurological assessment. The WB of muscle biopsy performed at 28 months of age showed a normal quantity and pattern of bands for calpain 3. Despite this finding, on molecular analysis she was found to be a compound heterozygote for two mutations of the calpain 3 (CAPN3) gene (R110X and G222R). Autocatalytic activity assay showed a loss of function of calpain 3. This is the first genetically confirmed case of very early onset calpainopathy with a normal amount of protein at WB. Molecular analysis is also suggested in very young patients with normal WB.