Genome sequence data can be used to analyze genome plasticity by whole genome PCR scanning. Small sized chromosomes can indeed be fully amplified by long-range PCR with a set of primers designed using a reference strain and applied to several other strains. Analysis of the resulting patterns can reveal the genome plasticity. To facilitate such analysis, we have developed GenoFrag, a software package for the design of primers optimized for whole genome scanning by long-range PCR. GenoFrag was developed for the analysis of Staphylococcus aureus genome plasticity by whole genome amplification in approximately 10 kb-long fragments. A set of primers was generated from the genome sequence of S.aureus N315, employed here as a reference strain. Two subsets of primers were successfully used to amplify two portions of the N315 chromosome. This experimental validation demonstrates that GenoFrag is a robust and reliable tool for primer design and that whole genome PCR scanning can be envisaged for the analysis of genome diversity in S.aureus, one of the major public health concerns worldwide.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373259 | PMC |
| http://dx.doi.org/10.1093/nar/gkg928 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
The GAA repeat expansion is a major cause of ataxia in the Cypriot population.
Brain Commun
January 2025
Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus.
Dominantly inherited intronic GAA repeat expansions in the fibroblast growth factor 14 gene have recently been shown to cause spinocerebellar ataxia 27B. Currently, the pathogenic threshold of (GAA) repeat units is considered highly penetrant, while (GAA) is likely pathogenic with reduced penetrance. This study investigated the frequency of the GAA repeat expansion and the phenotypic profile in a Cypriot cohort with unresolved late-onset cerebellar ataxia.
View Article and Find Full Text PDFRHCE genotyping using next generation sequencing: Allele specific reference sequences.
Transfusion
December 2024
School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK.
Background: The Rh blood group system (ISBT004) is encoded by two homologous genes, RHD and RHCE. Polymorphism in these two genes gives rise to 56 antigens, which are highly immunogenic and clinically significant. This study extended previous work on the establishment of RHD allele specific reference sequences using next generation sequencing (NGS) with the Ion Personal Genome Machine (Ion PGM) to sequence the complete RHCE gene.
View Article and Find Full Text PDFResistome in the indoor dust samples from workplaces and households: a pilot study.
Front Cell Infect Microbiol
December 2024
RECETOX, Faculty of Science, Masaryk University, Brno, Czechia.
The antibiotic resistance genes (ARGs) limit the susceptibility of bacteria to antimicrobials, representing a problem of high importance. Current research on the presence of ARGs in microorganisms focuses mainly on humans, livestock, hospitals, or wastewater. However, the spectrum of ARGs in the dust resistome in workplaces and households has gone relatively unexplored.
View Article and Find Full Text PDFAlu-Mediated Duplication and Deletion of Exon 11 Are Frequent Mechanisms of Inactivation, Predisposing Individuals to Hereditary Breast-Ovarian Cancer Syndrome.
Cancers (Basel)
November 2024
Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, 50139 Florence, Italy.
Background/objective: Large genomic rearrangements of gene, particularly deletions and duplications, have been linked to hereditary breast-ovarian cancer. Our research specifically focuses on delineating the intronic breakpoints associated with rearrangements of exon 11, which is crucial for understanding the mechanisms underlying these genomic changes in patients with hereditary breast and ovarian syndrome.
Methods: By using next-generation sequencing, we identified one duplication and three deletions of exon 11, confirmed by Multiplex Ligation-Dependent Probe Amplification analysis.
The Full-Length Genomic Sequence of the HLA-B*40:298:02 Allele.
HLA
December 2024
Laboratory of Cellular and Molecular Biology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, China.
Article Synopsis
- HLA-B*40:298:02 and HLA-B*40:01:01 are two variations of the HLA-B gene.
- The difference between them includes eight nucleotide changes that occur from exon 1 to intron 6.
- These differences in the gene can have implications for immune responses and disease susceptibility.
Want AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!