Current Issue : April - June Volume : 2019 Issue Number : 2 Articles : 5 Articles
Skeletogenesis, remodeling, and maintenance in adult tissues are regulated by sequential\nactivation of genes coding for specific transcription factors. The conserved Homeobox genes\n(HOX, in humans) are involved in several skeletal pathologies. Osteoarthritis (OA) is characterized\nby homeostatic alterations of cartilage and bone synthesis, resulting in cartilage destruction and\nincreased bone formation. We postulate that alterations in HOX expression in Mesenchymal Stem\ncells (MSCs) are likely one of the causes explaining the homeostatic alterations in OA and that\nthis altered expression could be the result of epigenetic regulation. The expression of HOX genes\nin osteoarthritic-derived MSCs was screened using PCR arrays. Epigenetic regulation of HOX\nwas analyzed measuring the degree of DNA methylation in their promoters. We demonstrate the\ndownregulated expression of HOXA9 and HOXC8 in OA-MSCs. However, their expression does\nnot correlate with promoter methylation status, suggesting that other epigenetic mechanisms could\nbe implicated in the regulation of HOX expression. Studies on the role of these genes under active\ndifferentiation conditions need to be addressed for a better knowledge of the mechanisms regulating\nthe expression of HOX, to allow a better understanding of OA pathology and to define possible\nbiomarkers for therapeutic treatment....
Parkinsonâ??s disease (PD) is a chronic, progressive neurodegenerative disease characterized\nby both motor and nonmotor features. The diagnose of PD is based on a review of patientsâ?? signs and\nsymptoms, and neurological and physical examinations. So far, no tests have been devised that can\nconclusively diagnose PD. In this study, we explore both microRNA and gene biomarkers for PD.\nMicroarray gene expression profiles for PD patients and healthy control are analyzed using a principal\ncomponent analysis (PCA)-based unsupervised feature extraction (FE). 244 genes are selected to be\npotential gene biomarkers for PD. In addition, we implement these genes into Kyoto Encyclopedia of\nGenes and Genomes (KEGG) pathways, and find that the 15 microRNAs (miRNAs), hsa-miR-92a-3p,\n16-5p, 615-3p, 877-3p, 100-5p, 320a, 877-5p, 23a-3p, 484, 23b-3p, 15a-5p, 324-3p, 19b-3p, 7b-5p and\n505-3p, significantly target these 244 genes. These miRNAs are shown to be significantly related to\nPD. This reveals that both selected genes and miRNAs are potential biomarkers for PD....
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Background: Targeted resequencing has become the most used and cost-effective approach for identifying\ncausative mutations of Mendelian diseases both for diagnostics and research purposes. Due to very rapid\ntechnological progress, NGS laboratories are expanding their capabilities to address the increasing number of\nanalyses. Several open source tools are available to build a generic variant calling pipeline, but a tool able to\nsimultaneously execute multiple analyses, organize, and categorize the samples is still missing.\nResults: Here we describe VarGenius, a Linux based command line software able to execute customizable\npipelines for the analysis of multiple targeted resequencing data using parallel computing. VarGenius provides\na database to store the output of the analysis (calling quality statistics, variant annotations, internal allelic\nvariant frequencies) and sample information (personal data, genotypes, phenotypes). VarGenius can also\nperform the â??joint analysisâ? of hundreds of samples with a single command, drastically reducing the time for\nthe configuration and execution of the analysis.\nVarGenius executes the standard pipeline of the Genome Analysis Tool-Kit (GATK) best practices (GBP) for germinal\nvariant calling, annotates the variants using Annovar, and generates a user-friendly output displaying the results\nthrough a web page.\nVarGenius has been tested on a parallel computing cluster with 52 machines with 120GB of RAM each. Under this\nconfiguration, a 50M whole exome sequencing (WES) analysis for a family was executed in about 7 h (trio or quartet); a\njoint analysis of 30 WES in about 24 h and the parallel analysis of 34 single samples from a 1M panel in about 2 h.\nConclusions: We developed VarGenius, a â??masterâ? tool that faces the increasing demand of heterogeneous\nNGS analyses and allows maximum flexibility for downstream analyses. It paves the way to a different kind\nof analysis, centered on cohorts rather than on singleton. Patient and variant information are stored into the\ndatabase and any output file can be accessed programmatically. VarGenius can be used for routine analyses\nby biomedical researchers with basic Linux skills providing additional flexibility for computational biologists to\ndevelop their own algorithms for the comparison and analysis of data.\nThe software is freely available at: https://github.com/frankMusacchia/VarGenius...
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