Survey of Italian Pediatricians on awareness, experiences and beliefs regarding direct-to-consumer genetic testing in minors

Background: Our study wanted to assess Italian pediatricians’ awareness, experience and beliefs regarding directto-consumer (DTC) genetic tests (GT) in minors, with a focus on those for predisposition to complex disease, lyfestyle, athletic ability and other inborn talents. Methods: A 28-item questionnaire was administered through the SurveyMonkey® web platform to the 9,086 members of the Italian Society of Pediatrics for which a valid email address was available. The survey was opened from April through November 2017. Statistical analyses were performed using the Graphpad software package. Results: 36.2% of the 442 respondents were aware of DTC-GT, but only 23.1% of them felt adequately prepared to meet families’ information needs. The first three sources of knowledge were the Internet (20.98%), magazines/ newspapers (16.78%) and TV/Radio (14.33%), while companies’ direct marketing activity influenced knowledge only in 2.45% of the cases. Only 16.4% of the aware respondents had been already approached for advice. More than 95% of the pediatricians who were aware would not advise DTC-GT for lifestyle, athletic performance or other inborn skills. 69.2% was unfavourable to susceptibility tests for complex diseases. Most of them expressed an interest in learning more and indicated as preferred sources of information public policies issued by professional societies. Conclusion: The low awareness and experience and the vendors’ tiny contribution to knowledge suggest a still limited penetration of DTC-GT companies in Italy. A great interest in learning more was found. Scientific societies are best positioned to support health professionals in this educational goal thanks to their role of trusted sources of information and guidance.&nbsp

Detecting common copy number variants in high-throughput sequencing data by using JointSLM algorithm

The discovery of genomic structural variants (SVs), such as copy number variants (CNVs), is essential to understand genetic variation of human populations and complex diseases. Over recent years, the advent of new high-throughput sequencing (HTS) platforms has opened many opportunities for SVs discovery, and a very promising approach consists in measuring the depth of coverage (DOC) of reads aligned to the human reference genome. At present, few computational methods have been developed for the analysis of DOC data and all of these methods allow to analyse only one sample at time. For these reasons, we developed a novel algorithm (JointSLM) that allows to detect common CNVs among individuals by analysing DOC data from multiple samples simultaneously. We test JointSLM performance on synthetic and real data and we show its unprecedented resolution that enables the detection of recurrent CNV regions as small as 500 bp in size. When we apply JointSLM to analyse chromosome one of eight genomes with different ancestry, we identify 3000 regions with recurrent CNVs of different frequency and size: hierarchical clustering on these regions segregates the eight individuals in two groups that reflect their ancestry, demonstrating the potential utility of JointSLM for population genetics studies

Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript

Abstract Motivation: The discovery of novel gene fusions can lead to a better comprehension of cancer progression and development. The emergence of deep sequencing of trancriptome, known as RNA-seq, has opened many opportunities for the identification of this class of genomic alterations, leading to the discovery of novel chimeric transcripts in melanomas, breast cancers and lymphomas. Nowadays, few computational approaches have been developed for the detection of chimeric transcripts. Although all of these computational methods show good sensitivity, much work remains to reduce the huge number of false-positive calls that arises from this analysis. Results: We proposed a novel computational framework, named chimEric tranScript detection algorithm (EricScript), for the identification of gene fusion products in paired-end RNA-seq data. Our simulation study on synthetic data demonstrates that EricScript enables to achieve higher sensitivity and specificity than existing methods with noticeably lower running times. We also applied our method to publicly available RNA-seq tumour datasets, and we showed its capability in rediscovering known gene fusions. Availability: The EricScript package is freely available under GPL v3 license at http://ericscript.sourceforge.net. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Microvascular function is selectively impaired in patients with hypertrophic cardiomyopathy and sarcomere myofilament gene mutations.

ObjectivesThe purpose of this study was to assess myocardial blood flow (MBF) using positron emission tomography in patients with hypertrophic cardiomyopathy (HCM) according to genetic status.BackgroundCoronary microvascular dysfunction is an important feature of HCM, associated with ventricular remodeling and heart failure. We recently demonstrated the increased prevalence of systolic dysfunction in patients with HCM with sarcomere myofilament gene mutations and postulated an association between genetic status and coronary microvascular dysfunction.MethodsMaximum MBF (intravenous dipyridamole, 0.56 mg/kg; Dip-MBF) was measured using 13N-labeled ammonia in 61 patients with HCM (age 38 ± 14 years), genotyped by automatic DNA sequencing of 8 myofilament-encoding genes (myosin-binding protein C, beta-myosin heavy chain, regulatory and essential light chains, troponin T, troponin I, troponin C, alpha-tropomyosin, and alpha-actin). In 35 patients, cardiac magnetic resonance imaging was performed.ResultsFifty-three mutations were identified in 42 of the 61 patients (genotype positive; 69%). Despite similar clinical profiles, genotype-positive patients with HCM showed substantially lower Dip-MBF compared with that of genotype-negative patients (1.7 ± 0.6 ml/min/g vs. 2.4 ± 1.2 ml/min/g; p < 0.02). A Dip-MBF <1.5 ml/min/g had 81% positive predictive value for genotype-positive status and implied a 3.5-fold independent increase in likelihood of carrying myofilament gene mutations (hazard ratio: 3.52; 95% confidence interval: 1.05 to 11.7; p = 0.04). At cardiac magnetic resonance imaging, the prevalence of late gadolinium enhancement was greater in genotype-positive patients (22 of 23 [96%] compared with 8 of 12 [67%] genotype-negative patients; p = 0.038).ConclusionsPatients with HCM with sarcomere myofilament mutations are characterized by more severe impairment of microvascular function and increased prevalence of myocardial fibrosis, compared with genotype-negative individuals. These findings suggest a direct link between sarcomere gene mutations and adverse remodeling of the microcirculation in HCM, accounting for the increased long-term prevalence of ventricular dysfunction and heart failure in genotype-positive patients

Using a calibration experiment to assess gene-specific information: full Bayesian and empirical Bayesian models for two-channel microarray data.

MOTIVATION: Microarray studies permit to quantify expression levels on a global scale by measuring transcript abundance of thousands of genes simultaneously. A difficulty when analysing expression measures is how to model variability for the whole set of genes. It is usually unrealistic to assume a common variance for each gene. Several approaches to model gene-specific variances are proposed. We take advantage of calibration experiments, in which the probes hybridized on the two channels come from the same population (self-self experiment). In this case it is possible to estimate the gene-specific variance, to be incorporated in comparative experiments on the same tissue, cellular line or species. RESULTS: We present two approaches to introduce prior information on gene-specific variability from a calibration experiment: an empirical Bayes model and a full Bayesian hierarchical model. We apply the methods in the analysis of human lipopolysaccharide-stimulated leukocyte experiments. AVAILABILITY: The calculations are implemented in WinBugs. The codes are available on request from the authors

Draft genome sequence of Proteus mirabilis NO-051/ 03, representative of a multidrug-resistant clone spreading in Europe and expressing the CMY-16 AmpC-type &#946;-lactamase

Proteus mirabilis NO-051/03, representative of a multidrug-resistant clone expressing the CMY-16 AmpC-type β-lactamase and circulating in Europe since 2003, was sequenced by a MiSeq platform using a paired-end approach. The genome was assembled in 100 scaffolds with a total length of 4,197,318 bp. Analysis of the draft genome sequence revealed the presence of several acquired resistance determinants to β-lactams, aminoglycosides, phenicols, tetracyclines, trimethoprim, and sulfonamides, of one plasmid replicon, and of a type I-E clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein (Cas) adaptive immune system

EX-HOM (EXome HOMozygosity): A Proof of Principle

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Estimate of tissue composition in malignant and benign breast lesions by time-domain optical mammography

partially_open10noThe optical characterization of malignant and benign breast lesions is presented. Time-resolved transmittance measurements were performed in the 630-1060 nm range by means of a 7-wavelength optical mammograph, providing both imaging and spectroscopy information. A total of 62 lesions were analyzed, including 33 malignant and 29 benign lesions. The characterization of breast lesions was performed applying a perturbation model based on the high-order calculation of the pathlength of photons inside the lesion, which led to the assessment of oxy- and deoxy- hemoglobin, lipids, water and collagen concentrations. Significant variations between tumor and healthy tissue were observed in terms of both absorption properties and constituents co ncentration. In particular, benign lesions and tumors show a statistically significant discrimination in terms of absorption at several wavelengths and also in terms of oxy-hemoglobin and collagen content.G. Quarto; L. Spinelli; A. Pifferi; A. Torricelli; R. Cubeddu; F. Abbate; N. Balestreri; S. Menna; E. Cassano; P. TaroniQuarto, Giovanna; Spinelli, Lorenzo; Pifferi, ANTONIO GIOVANNI; Torricelli, Alessandro; Cubeddu, Rinaldo; F., Abbate; N., Balestreri; S., Menna; E., Cassano; Taroni, Paol