Advantages of a next generation sequencing targeted approach for the molecular diagnosis of retinoblastoma.

BACKGROUND: Retinoblastoma (RB) is the most common malignant childhood tumor of the eye and results from inactivation of both alleles of the RB1 gene. Nowadays RB genetic diagnosis requires classical chromosome investigations, Multiplex Ligation-dependent Probe Amplification analysis (MLPA) and Sanger sequencing. Nevertheless, these techniques show some limitations. We report our experience on a cohort of RB patients using a combined approach of Next-Generation Sequencing (NGS) and RB1 custom array-Comparative Genomic Hybridization (aCGH). METHODS: A total of 65 patients with retinoblastoma were studied: 29 cases of bilateral RB and 36 cases of unilateral RB. All patients were previously tested with conventional cytogenetics and MLPA techniques. Fifty-three samples were then analysed using NGS. Eleven cases were analysed by RB1 custom aCGH. One last case was studied only by classic cytogenetics. Finally, it has been tested, in a lab sensitivity assay, the capability of NGS to detect artificial mosaicism series in previously recognized samples prepared at 3 different mosaicism frequencies: 10, 5, 1 %. RESULTS: Of the 29 cases of bilateral RB, 28 resulted positive (96.5 %) to the genetic investigation: 22 point mutations and 6 genomic rearrangements (four intragenic and two macrodeletion). A novel germline intragenic duplication, from exon18 to exon 23, was identified in a proband with bilateral RB. Of the 36 available cases of unilateral RB, 8 patients resulted positive (22 %) to the genetic investigation: 3 patients showed point mutations while 5 carried large deletion. Finally, we successfully validated, in a lab sensitivity assay, the capability of NGS to accurately measure level of artificial mosaicism down to 1 %. CONCLUSIONS: NGS and RB1-custom aCGH have demonstrated to be an effective combined approach in order to optimize the overall diagnostic procedures of RB. Custom aCGH is able to accurately detect genomic rearrangements allowing the characterization of their extension. NGS is extremely accurate in detecting single nucleotide variants, relatively simple to perform, cost savings and efficient and has confirmed a high sensitivity and accuracy in identifying low levels of artificial mosaicisms.

Diagnosis of Noonan syndrome and related disorders using target next generation sequencing.

BACKGROUND: Noonan syndrome is an autosomal dominant developmental disorder with a high phenotypic variability, which shares clinical features with other rare conditions, including LEOPARD syndrome, cardiofaciocutaneous syndrome, Noonan-like syndrome with loose anagen hair, and Costello syndrome. This group of related disorders, so-called RASopathies, is caused by germline mutations in distinct genes encoding for components of the RAS-MAPK signalling pathway. Due to high number of genes associated with these disorders, standard diagnostic testing requires expensive and time consuming approaches using Sanger sequencing. In this study we show how targeted Next Generation Sequencing (NGS) technique can enable accurate, faster and cost-effective diagnosis of RASopathies. METHODS: In this study we used a validation set of 10 patients (6 positive controls previously characterized by Sanger-sequencing and 4 negative controls) to assess the analytical sensitivity and specificity of the targeted NGS. As second step, a training set of 80 enrolled patients with a clinical suspect of RASopathies has been tested. Targeted NGS has been successfully applied over 92% of the regions of interest, including exons for the following genes: PTPN11, SOS1, RAF1, BRAF, HRAS, KRAS, NRAS, SHOC, MAP2K1, MAP2K2, CBL. RESULTS: All expected variants in patients belonging to the validation set have been identified by targeted NGS providing a detection rate of 100%. Furthermore, all the newly detected mutations in patients from the training set have been confirmed by Sanger sequencing. Absence of any false negative event has been excluded by testing some of the negative patients, randomly selected, with Sanger sequencing. CONCLUSION: Here we show how molecular testing of RASopathies by targeted NGS could allow an early and accurate diagnosis for all enrolled patients, enabling a prompt diagnosis especially for those patients with mild, non-specific or atypical features, in whom the detection of the causative mutation usually requires prolonged diagnostic timings when using standard routine. This approach strongly improved genetic counselling and clinical management.

Adopting European Network for Health Technology Assessments (EunetHTA) core model for diagnostic technologies for improving the accuracy and appropriateness of blood gas analyzers' assessment.

BACKGROUND: Point-of-care testing (POCT) is a successful methodology for meeting clinical expectations of rapid and accurate results. Scientific literature has moreover highlighted and confirmed the necessity of individuating the best technological solution, in accordance with clinical requirements and contextualized to the whole health organization, where it will be implemented. Health Technology Assessment (HTA) can assist in reaching an appropriate and contextualized decision on a health technology. The aim of this study is to adapt a HTA core model for improving the evaluation of a POCT technology: blood gas analyzers. METHODS: The European Network for Health Technology Assessment (EUnetHTA) core model for diagnostic technologies was applied for evaluating globally marketed blood gas analyzers. Evaluation elements were defined according to available literature and validated using the Delphi method. RESULTS: A HTA model of 71 issues, subdivided into 26 topics and 10 domains, was obtained by interviewing 11 healthcare experts over two rounds of Delphi questionnaires. Ten context parameters were identified in order to define the initial scenario from which the technology assessment was to begin. CONCLUSIONS: The model presented offers a systematic and objective structure for the evaluation of blood gas analyzers, which may play a guidance role for healthcare operators approaching the evaluation of such technologies thus improving, in a contextualized fashion, the appropriateness of purchasing.

Common conditions of use elements. Atomic concepts for consistent and effective information governance.

Myriad policy, ethical and legal considerations underpin the sharing of biological resources, implying the need for standardised and yet flexible ways to digitally represent diverse 'use conditions'. We report a core lexicon of terms that are atomic, non-directional 'concepts of use', called Common Conditions of use Elements. This work engaged biobanks and registries relevant to the European Joint Programme for Rare Diseases and aimed to produce a lexicon that would have generalised utility. Seventy-six concepts were initially identified from diverse real-world settings, and via iterative rounds of deliberation and user-testing these were optimised and condensed down to 20 items. To validate utility, support software and training information was provided to biobanks and registries who were asked to create Sharing Policy Profiles. This succeeded and involved adding standardised directionality and scope annotations to the employed terms. The addition of free-text parameters was also explored. The approach is now being adopted by several real-world projects, enabling this standard to evolve progressively into a universal basis for representing and managing conditions of use.

Parcel-based connectivity analysis of fMRI data for the study of epileptic seizure propagation.

The aim of this work is to improve fMRI Granger Causality Analysis (GCA) by proposing and comparing two strategies for defining the topology of the networks among which cerebral connectivity is measured and to apply fMRI GCA for studying epileptic seizure propagation. The first proposed method is based on information derived from anatomical atlas only; the other one is based on functional information and employs an algorithm of hierarchical clustering applied to fMRI data directly. Both methods were applied to signals recorded during seizures on a group of epileptic subjects and two connectivity matrices were obtained for each patient. The performances of the different parcellation strategies were evaluated in terms of their capability to recover information about the source and the sink of the network (i.e., the starting and the ending point of the seizure propagation). The first method allows to clearly identify the seizure onset in all patients, whereas the network sources are not so immediately recognizable when the second method was used. Nevertheless, results obtained using functional clustering do not contradict those obtained with the anatomical atlas and are able to individuate the main pattern of propagation. In conclusion, the way nodes are defined can influence the easiness of identification of the epileptogenic focus but does not produce contradictory results showing the effectiveness of proposed approach to formulate hypothesis about seizure propagation at least in the early phase of investigation.

Gray matter decrease distribution in the early stages of Anorexia Nervosa restrictive type in adolescents.

Few studies have used Voxel-Based Morphometry (VBM) to examine brain structure in Anorexia Nervosa patients. The purpose of the present study was to investigate a sample of Anorexia Nervosa restrictive type (AN-r) adolescent patients in the early stages of the illness, using VBM in order to characterize morphometric gray matter (GM) changes. Participants were 16 AN-r female patients (with no other psychiatric disorders) whose AN-r had been in progress for less than 12 months and 16 age-matched healthy female subjects. High-resolution T1-weighted magnetic resonance images were preprocessed according to the optimized VBM method, and statistically analyzed. The analyses revealed a significant global GM decrease in the AN-r patients; furthermore, a significant region-specific decrease in GM volume was found bilaterally in the middle cingulate cortex, the precuneus, and the inferior and superior parietal lobules. The significant early GM decrease in the aforementioned regions in AN-r adolescent patients suggests that there might be a region-specific GM vulnerability that could play a role in the pathophysiology of the disease. Given that these regions are also involved in the manipulation of mental images and the mental representation of the self, this might explain the presence of a distorted body image in these patients.

[The biological resources and molecule archives organization: turn a need into an opportunity for the Smart Specialization Strategy of the Lazio region.] / Organizzare risorse biologiche e archivi di molecole: trasformare una necessità in opportunità per la Smart Specialisation Strategy della Regione Lazio.

Smart Specialization Strategy (S3) of Lazio defines smart specialization strategies to bring out the excellence of the territory with prospects of success on the global market. Chemical-pharmaceutical, biomedical and biotechnological field is one of the 7 sectors considered of greatest interest for the S3. Key engine of biotechnology development are biological materials and associated data, stored in biobanks. However, to ensure that the research and product development carried out with that resources gives statistically significant and reproducible results, it is essential that they are collected, manipulated and stored using standardized and traced methods. Implementation of the recent published standard ISO 20387- "Biotechnology-Biobanking-General requirements for biobanking" is bridging biobanks toward to storage and distribution of qualified biological material only. Human biobanks are also an essential part of the assistance and care of the citizen and constitute an unavoidable cost of the regional health system. However, biobanks organization, rationalization of their territorial distribution, completion of the process of recognition and regional accreditation, parallel to the implementation of the offer of remunerated services for biobanking, can turn the cost of the necessary preservation of the samples, into an opportunity of territorial development. The paper describes the necessity, shared by a working group represented by several Lazio biobanks, of including biobank activities in the virtuous circle designed by the S3,concretizing the framework prefigured by the S3 document on infrastructures for research, innovation and technology transfer. To allow inclusion of biobank activities in the virtuous circle, we underline the need to quickly start the process of recognition of the territorial research biobanks, to implement at regional level the process of optimization and rationalization of the management of biological samples, in accordance with the international harmonization standards and with the territorial indications of sustainability.

Identifying the dynamics of actin and tubulin polymerization in iPSCs and in iPSC-derived neurons.

The development of the nervous system requires cytoskeleton-mediated processes coordinating self-renewal, migration, and differentiation of neurons. It is not surprising that many neurodevelopmental problems and neurodegenerative disorders are caused by deficiencies in cytoskeleton-related genes. For this reason, we focus on the cytoskeletal dynamics in proliferating iPSCs and in iPSC-derived neurons to better characterize the underpinnings of cytoskeletal organization looking at actin and tubulin repolymerization studies using the cell permeable probes SiR-Actin and SiR-Tubulin. During neurogenesis, each neuron extends an axon in a complex and changing environment to reach its final target. The dynamic behavior of the growth cone and its capacity to respond to multiple spatial information allows it to find its correct target. We decided to characterize various parameters of the actin filaments and microtubules. Our results suggest that a rapid re-organization of the cytoskeleton occurs 45 minutes after treatments with de-polymerizing agents in iPSCs and 60 minutes in iPSC-derived neurons in both actin filaments and microtubules. The quantitative data confirm that the actin filaments have a primary role in the re-organization of the cytoskeleton soon after de-polymerization, while microtubules have a major function following cytoskeletal stabilization. In conclusion, we investigate the possibility that de-polymerization of the actin filaments may have an impact on microtubules organization and that de-polymerization of the microtubules may affect the stability of the actin filaments. Our results suggest that a reciprocal influence of the actin filaments occurs over the microtubules and vice versa in both in iPSCs and iPSC-derived neurons.

Independent Component Analysis of EEG-fMRI data for studying epilepsy and epileptic seizures.

Here we present a method for classifying fMRI independent components (ICs) by using an optimized algorithm for the individuation of noisy signals from sources of interest. The method was applied to estimate brain activations from combined EEG-fMRI data for the exploration of epilepsy. Spatial ICA was performed using the above-mentioned optimized algorithm and other three popular algorithms. ICs were sorted considering the value: of the coefficients of determination R2, obtained from the multiple regression analysis with morphometric maps of cerebral matter; of the kurtosis, which features the signal energy. The validation of the method was performed comparing the brain activations obtained with those resulted using the General Linear Model (GLM). The ICA-derived activations in different datasets comprised subareas of the GLM-revealed activations, even if the volume and the shape of activated areas do not correspond exactly. The method proposed also detects additional negative regions implicated in a default mode of brain activity, and not clearly identified by GLM. Compared with a traditional GLM approach, the ICA one provides a flexible way to analyze fMRI data that reduces the assumptions placed upon the hemodynamic response of the brain and the temporal constrains.