Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2

Copy Number Variants (CNVs) are structural rear- rangements contributing to phenotypic variation that have been proved to be associated with many dis- ease states. Over the last years, the identification of CNVs from whole-exome sequencing (WES) data has become a common practice for research and clinical purpose and, consequently, the demand for more and more efficient and accurate methods has increased. In this paper, we demonstrate that more than 30% of WES data map outside the targeted re- gions and that these reads, usually discarded, can be exploited to enhance the identification of CNVs from WES experiments. Here, we present EXCAVATOR2, the first read count based tool that exploits all the reads produced by WES experiments to detect CNVs with a genome-wide resolution. To evaluate the per- formance of our novel tool we use it for analysing two WES data sets, a population data set sequenced by the 1000 Genomes Project and a tumor data set made of bladder cancer samples. The results obtained from these analyses demonstrate that EXCAVATOR2 out- performs other four state-of-the-art methods and that our combined approach enlarge the spectrum of detectable CNVs from WES data with an unprece- dented resolution

Surgical procedures as a major risk factor for chronic hepatitis C virus infection in Italy: Evidence from a case-control study

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Results of case-control studies supportthe association between contact lens useand Acanthamoeba keratitis

Acanthamoeba keratitis (AK) is ever more frequently reported in industrialized countries. The loss of the corneal surface integrity consequent to secondary microtrauma produced by the use of contact lens (CL) favors the penetration of the parasite into the corneal tissue. A scientific review was performed to investigate the association of CL wear as an Acanthamoeba keratitis (AK) risk factor. A computerized screening of 7834 Medline articles (4623 from PubMed; 3211 from Scopus) used a strict selection criteria of case-control studies involving CL wear and/or trauma. The search yielded five case-control studies published from 1995 to 2012. All studies included showed a statistically significant positive association between AK and CL use, with a combined odds ratio (OR) of 10.21 (95%, confidence intervals [CI]; 3.57-27.64). All studies included showed a statistically significant positive association between AK and CL use, though with differing OR values. Though rare, AK should be held in higher consideration when ophthalmologists are faced with CL users exhibiting simplex-like lesions associated with circular stromal infiltrates and disproportionate ocular pain in respect to the objective clinical picture.Abstract BACKGROUND: Acanthamoeba keratitis (AK) is ever more frequently reported in industrialized countries. The loss of the corneal surface integrity consequent to secondary microtrauma produced by the use of contact lens (CL) favors the penetration of the parasite into the corneal tissue. OBJECTIVES: A scientific review was performed to investigate the association of CL wear as an Acanthamoeba keratitis (AK) risk factor. METHODS: A computerized screening of 7834 Medline articles (4623 from PubMed; 3211 from Scopus) used a strict selection criteria of case-control studies involving CL wear and/or trauma. RESULTS: The search yielded five case-control studies published from 1995 to 2012. All studies included showed a statistically significant positive association between AK and CL use, with a combined odds ratio (OR) of 10.21 (95%, confidence intervals [CI]; 3.57-27.64). STATISTICAL ANALYSIS: All studies included showed a statistically significant positive association between AK

Characterization and identification of hidden rare variants in the human genome

BackgroundBy examining the genotype calls generated by the 1000 Genomes Project we discovered that the human reference genome GRCh37 contains almost 20,000 loci in which the reference allele has never been observed in healthy individuals and around 70,000 loci in which it has been observed only in the heterozygous state.ResultsWe show that a large fraction of this rare reference allele (RRA) loci belongs to coding, functional and regulatory elements of the genome and could be linked to rare Mendelian disorders as well as cancer. We also demonstrate that classical germline and somatic variant calling tools are not capable to recognize the rare allele when present in these loci. To overcome such limitations, we developed a novel tool, named RAREVATOR, that is able to identify and call the rare allele in these genomic positions. By using a small cancer dataset we compared our tool with two state-of-the-art callers and we found that RAREVATOR identified more than 1,500 germline and 22 somatic RRA variants missed by the two methods and which belong to significantly mutated pathways.ConclusionsThese results show that, to date, the investigation of around 100,000 loci of the human genome has been missed by re-sequencing experiments based on the GRCh37 assembly and that our tool can fill the gap left by other methods. Moreover, the investigation of the latest version of the human reference genome, GRCh38, showed that although the GRC corrected almost all insertions and a small part of SNVs and deletions, a large number of functionally relevant RRAs still remain unchanged. For this reason, also future resequencing experiments, based on GRCh38, will benefit from RAREVATOR analysis results. RAREVATOR is freely available at http://sourceforge.net/projects/rarevator

Pleiotropic effects of anti-thrombotic therapies: have direct oral anticoagulants any anti-inflammatory effect?

Direct oral anticoagulants (DOACs) are currently recommended by European guidelines as the first line therapy for both stroke prevention in patients with atrial fibrillation (AF) and the prevention and the treatment of venous thromboembolism (VTE). Recently, it has been speculated that DOACs have anti-inflammatory capabilities in reducing the abnormal release of pro-inflammatory factors in addition to inhibiting the activation of factor X or factor II of the coagulation cascade. However, this hypothesis is based on limited pathophysiological data with small sample size, often on in vitro studies. Real-world, in vivo, and large clinical data are scarce. The aim of the present study was the evaluation of the possible anti-inflammatory and anti-proliferative effects of DOACs treatment in a cohort of patients affected by AF or VTE, by analyzing an extensive panel of cytokines and molecules involved in the process of vascular and tissue remodeling. Our data evidenced that DOACs treatment is associated with variations in systemic inflammation markers and in metalloproteinases. Further studies with larger number of patients are required to confirm these data

Prognostic Relevance of Multi-Antigenic Myeloma-Specific T-Cell Assay in Patients with Monoclonal Gammopathies

: Multiple Myeloma (MM) typically originates from underlying precursor conditions, known as Monoclonal Gammopathy of Undetermined Significance (MGUS) and Smoldering Multiple Myeloma (SMM). Validated risk factors, related to the main features of the clonal plasma cells, are employed in the current prognostic models to assess long-term probabilities of progression to MM. In addition, new prognostic immunologic parameters, measuring protective MM-specific T-cell responses, could help to identify patients with shorter time-to-progression. In this report, we described a novel Multi-antigenic Myeloma-specific (MaMs) T-cell assay, based on ELISpot technology, providing simultaneous evaluation of T-cell responses towards ten different MM-associated antigens. When performed during long-term follow-up (mean 28 months) of 33 patients with either MGUS or SMM, such deca-antigenic myeloma-specific immunoassay allowed to significantly distinguish between stable vs. progressive disease (p < 0.001), independently from the Mayo Clinic risk category. Here, we report the first clinical experience showing that a wide (multi-antigen), standardized (irrespective to patients' HLA), MM-specific T-cell assay may routinely be applied, as a promising prognostic tool, during the follow-up of MGUS/SMM patients. Larger studies are needed to improve the antigenic panel and further explore the prognostic value of MaMs test in the risk assessment of patients with monoclonal gammopathies

Surgical and survival outcomes with perioperative or neoadjuvant immune-checkpoint inhibitors combined with platinum-based chemotherapy in resectable NSCLC: A systematic review and meta-analysis of randomised clinical trials

: The use of neoadjuvant or perioperative anti-PD(L)1 was recently tested in multiple clinical trials. We performed a systematic review and meta-analysis of randomised trials comparing neoadjuvant or perioperative chemoimmunotherapy to neoadjuvant chemotherapy in resectable NSCLC. Nine reports from 6 studies were included. Receipt of surgery was more frequent in the experimental arm (odds ratio, OR 1.39) as was pCR (OR 7.60). EFS was improved in the experimental arm (hazard ratio, HR 0.55) regardless of stage, histology, PD-L1 expression (PD-L1 negative, HR 0.74) and smoking exposure (never smokers, HR 0.67), as was OS (HR 0.67). Grade > = 3 treatment-related adverse events were more frequent in the experimental arm (OR 1.22). The experimental treatment improved surgical outcomes, pCR rates, EFS and OS in stage II-IIIB, EGFR/ALK negative resectable NSCLC; confirmatory evidence is warranted for stage IIIB tumours and with higher maturity of the OS endpoint