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DNA microarray for STD pathogen detection

ABSTRACT: This work describes the development of the first microarray detection system that simultaneously identifies common pathogens associated with STDs from clinical samples, and paves the way for establishing a time-saving, accurate and high-throughput diagnostic tool.

ORGANISM(S): human papillomavirus 31 Alphapapillomavirus 13 Metamycoplasma hominis Mycoplasmoides genitalium human papillomavirus 58 Neisseria gonorrhoeae human papillomavirus 39 human papillomavirus 11 human papillomavirus 33 human papillomavirus 35 Human alphaherpesvirus 2 Human alphaherpesvirus 1 Human papillomavirus Chlamydia trachomatis human papillomavirus 18 Ureaplasma Human papillomavirus type 6 Human papillomavirus 16

PROVIDER: GSE69508 | GEO | 2015/12/31

SECONDARY ACCESSION(S): PRJNA285757

REPOSITORIES: GEO

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DNA microarray for STD pathogen detection

Project description:This work describes the development of the first microarray detection system that simultaneously identifies common pathogens associated with STDs from clinical samples, and paves the way for establishing a time-saving, accurate and high-throughput diagnostic tool. The target genes are 16S rRNA gene for N. gonorrhoeae, M. genitalium, M. hominism, and Ureaplasma, the major outer membrane protein gene (ompA) for C. trachomatis, the glycoprotein B gene (gB) for HSV; and the L1 gene for HPV. 34 probes that reproducibly detected multiple Legionella species with high specificity were included in the array.

2015-12-31 | E-GEOD-69508 | biostudies-arrayexpress

Antibody detection of translocations (ADOT) in Ewing Sarcoma

2012-01-31 | GSE35450 | GEO

Antibody detection of translocations (ADOT) in Ewing Sarcoma

Project description:We developed a new approach called antibody detection of translocations (ADOT) which combines a transcriptional microarray-based approach with a novel antibody-based detection method to detect translocations in cancer. ADOT allows for the accurate and sensitive identification of translocations and provides exon-level information about the fusion transcript. ADOT can detect translocations in poor quality unprocessed total RNA. We demonstrate the feasibility of ADOT by examples in which both known and unknown Ewing sarcoma translocations are identified from cell lines, tumor xenografts, and FFPE primary tumors. These results demonstrate that ADOT may be an effective approach for translocation analysis in clinical specimens with significant RNA degradation and may offer a novel diagnostic tool for translocation-based cancers. We designed oligonucleotide probes for each possible exon-exon combination between potential fusion partners and printed the DNA oligonucleotides on custom-designed microarrays. Total RNA from tumor cells or tissues was hybridized on the array. Bound RNA was detected with the S9.6 monoclonal antibody that recognizes RNA-DNA duplexes in a sequence-independent fashion,and detected with Cy3-labeled anti-mouse IgG.

2012-01-31 | E-GEOD-35450 | biostudies-arrayexpress

miRNA profiling of Macaca nemestrina plasma samples: before SIV infection and during acute infection

Project description:This study describes a circulating miRNA signature of acute retroviral infection, which may include candidate diagnostic or prognostic miRNAs for lentivirus-associated neurologic conditions.

2011-09-15 | GSE26057 | GEO

MIPP-Seq: Ultra-sensitive rapid detection and validation of low-frequency mosaic mutations

Project description:MIPP-Seq provides an ultra-sensitive, low-cost approach for detecting and validating known and novel mutations in a highly scalable system with broad utility spanning both research and clinical diagnostic testing applications. The scalability of MIPP-Seq allows for multiplexing mutations and samples, which dramatically reduce costs of variant validation when compared to methods like ddPCR. By leveraging the power of individual analyses of multiple unique and independent reactions, MIPP-Seq can validate and precisely quantitate extremely low AAFs across multiple tissues and mutational categories including both indels and SNVs. Furthermore, using Illumina sequencing technology, MIPP-seq provides a robust method for accurate detection of novel mutations at an extremely low AAF.

2021-01-30 | GSE165780 | GEO

Comparison between DiaPlexQ™ STI6 and GeneFinder™ STD I/STD II multiplex Real-time PCR Kits in the detection of six sexually transmitted disease pathogens.

Project description: Not available

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Proteomic profiling of serum extracellular vesicles identifies diagnostic markers for echinococcosis

Project description:In the present study, we employed a proteomics approach to identify parasite-derived proteins in the serum EVs from E. multilocularis-infected mice and assessed their diagnostic values. The study paves the way for the use of EVs to identify of diagnostic candidates and potentiates the applications of TER ATPase and TPx-1 in the early diagnosis and prognostic evaluation of echinococcosis.

2022-09-11 | PXD036031 | Pride

Dynamic host-pathogen interactions in pathogen-challenged chicken embryo fibroblasts cells with Marek’s Disease Virus using 3’ end enriched RNA-seq

Project description:Marek’s disease is a contagious lymphoproliferative disease of chickens and is a unique model of viral oncogenesis. Mapping changes or states over the course of infection for both host and pathogen would have the potential to generate important insights into dynamic host-pathogen interactions. Here we introduced 3’ end enriched RNA-seq as a novel method to study host-pathogen interactions in Marek’s disease virus challenged chicken embryo fibroblasts cells, which allowed accurate profiling of gene expression and alternative polyadenylation sites for host and pathogen simultaneously. We totally identified 476 differentially expressed genes and 437 APA switching genes in host, including switching in tandem 3’ UTRs and switching between coding region and 3’ UTR. Most of these genes were related to innate immunity, apoptosis and metabolism, but two sets of genes overlapped a little suggesting two complementary mechanisms for regulating gene expression during infection. In summary, our results gave a relatively comprehensive insight into dynamic host-pathogen interactions in gene transcription regulation during Marek’s disease virus infection and suggested that 3’ end enriched RNA-seq was a promising method to investigate global host-pathogen interactions.

2017-09-22 | GSE92567 | GEO

Keloid-specific gene expression profiling for accurate diagnostic and therapeutic applications.

Project description:Keloid-specific gene expression profiling for accurate diagnostic and therapeutic applications.

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The Microbial Detection Array Combined with Random Phi29-Amplification used as a Diagnostic Tool for Unbiased Virus Detection in Clinical Samples

Project description:A common technique used for sensitive and specific diagnostic virus detection in clinical samples is PCR. However, an unbiased diagnostic microarray containing probes for all human pathogens could replace hundreds of individual PCR-reactions and remove the need for a clear clinical hypothesis regarding a suspected pathogen. We have established such a diagnostic platform for unbiased random amplification and subsequent microarray identification of viral pathogens in clinical samples. We show that Phi29 polymerase-amplification of a diverse set of clinical samples generates enough viral material for successful identification by the Microbial Detection Array developed at the Lawrence Livermore National Laboratory, California, USA, demonstrating the potential of the microarray technique for broad-spectrum pathogen detection. We conclude that this method detects both DNA and RNA virus, present in the same sample, as well as differentiates between different virus subtypes. We propose this assay for unbiased diagnostic analysis of all viruses in clinical samples.

2011-04-14 | GSE28597 | GEO

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