DNA microarray technology and integrative viral genomics

Antimicrobial resistance (AMR) represents a real burden for the modern medicine. One of the most frecvently isolated hospital acquired (HA) pathogens wordlwide, is Methicillin resistant Staphylococcus aureus (MRSA). Recently not only HA, but also community-acquired MRSA (CA-MRSA) infections have been reported. A prospective study was performed between February 2009 and October 2010, with the aim to investigate bacterial resistance of CA-MRSA and HA-MRSA. DNA microarray technology has been used for the detection of 4 AMR genes for the studied MRSA strains. A number of 218 HA- S.aureus strains have been isolated, from which 89 (40. 82%) were MRSA. In the community, 1.553 S.aureus strains were isolated, out of which, 356 (22. 92%) were MRSA. From these, a number of 17 HA and 12 CA �MRSA strains have been analyzed by DNA microarray technology. From 100% phenotypically described HA- MRSA, we identified mecA gene in 10 strains (58. 83%). Other 6 strains (35. 29%) have been erm(A) positive and 4 (23. 53%) - tet(O) positive. 83. 33% (10 strains) from the CA strains had mecA gene, only one (8. 33%) was erm(A) positive and 4 (33. 33%) were erm(C) positive. DNA microarray is a method allowing the concomitant scan of multiple genes and can be done within a few hours. That type of rapid and reliable methods for antimicrobial sensitivity tests are important to start an appropriate therapy.

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DNA Microarray Technology in the Clinical Environment: The AmpliChip CYP450 Test for CYP2D6 and CYP2C19 Genotyping

CNS Spectrums ◽

10.1017/s1092852900020022 ◽

2009 ◽

Vol 14 (1) ◽

pp. 19-35 ◽

Cited By ~ 68

Author(s):

Jose de Leon ◽

Margaret T. Susce ◽

Maria Johnson ◽

Mike Hardin ◽

Lorraine Maw ◽

...

Keyword(s):

African Americans ◽

Dna Microarray ◽

Dna Sequences ◽

Psychiatric Patients ◽

Poor Metabolizers ◽

Microarray Technology ◽

Clinical Environment ◽

State Hospitals ◽

Cyp2c19 Gene ◽

Ultrarapid Metabolizers

ABSTRACTIntroduction: An important technological advance in genetic testing is the DNA microarray, which allows for the simultaneous testing of thousands of DNA sequences. The AmpliChip CYP450 Test employs this microarray technology for cytochrome P450 (CYP) 2D6 and CYP2C19 genotyping. Isoenzymes encoded by these genes are responsible for the metabolism of many widely prescribed drugs. The objectives of this study were to identify CYP2D6 and CYP2C19 alleles and phenotypes in a psychiatric patient population in Kentucky, and to describe practical issues associated with DNA microarray technology.Methods: A total of 4,532 psychiatric patients were recruited from three state hospitals in Kentucky. Whole blood, buccal swabs, or saliva samples were genotyped with the AmpliChip CYP450 Test to derive a predicted phenotype.Results: In this cohort, the overall prevalence of CYP2D6 poor metabolizers was 7.6% (95% CI 7%, 8.3%), 8.2% in the Caucasians (95% CI 7.4%, 9.1%) and 1.8% in the African Americans (95% CI 0.9%, 3.5%). The overall prevalence of CYP2D6 ultrarapid metabolizers was 1.5% (95% CI 1.2%, 1.9%), 1.5% in the Caucasians (95% CI 1.1%, 1.9%) and 2.0% in the African Americans (95% CI 1.1%, 3.7%). The overall prevalence of CYP2C19 poor metabolizers was 2.0% (95% CI 1.8%, 2.7%), 2.2% in Caucasians (95% CI 1.6%, 2.5%) and 4.0% in African Americans (95% CI 2.6%, 6.1%).Conclusion: We also propose a numeric system for expression of CYP2D6 and CYP2C19 enzyme activity to aid clinicians in determining treatment strategy for patients receiving therapeutics that are metabolized by the CYP2D6 or CYP2C19 gene products.

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Applications and Challenges of DNA Microarray Technology in Military Medical Research

Military Medicine ◽

10.7205/milmed.169.8.654 ◽

2004 ◽

Vol 169 (8) ◽

pp. 654-659 ◽

Cited By ~ 5

Author(s):

Sorin Draghici ◽

Dechang Chen ◽

Jaques Reifman

Keyword(s):

Medical Research ◽

Dna Microarray ◽

Microarray Technology

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Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing

The Open Microbiology Journal ◽

10.2174/1874285801610010176 ◽

2016 ◽

Vol 10 (1) ◽

pp. 176-182 ◽

Cited By ~ 8

Author(s):

Reza Ranjbar ◽

Payam Behzadi ◽

Caterina Mammina

Keyword(s):

Dna Microarray ◽

Francisella Tularensis ◽

High Specificity ◽

Cost Effective ◽

High Rate ◽

Molecular Diagnostic ◽

Microarray Technology ◽

Microarray Probe ◽

Specificity And Sensitivity ◽

Oligo Microarray

Background:Francisella tularensis(F. tularensis) is the etiological microorganism for tularemia. There are different forms of tularemia such as respiratory tularemia. Respiratory tularemia is the most severe form of tularemia with a high rate of mortality; if not treated. Therefore, traditional microbiological tools and Polymerase Chain Reaction (PCR) are not useful for a rapid, reliable, accurate, sensitive and specific diagnosis. But, DNA microarray technology does. DNA microarray technology needs to appropriate microarray probe designing.Objective:The main goal of this original article was to design suitable long oligo microarray probes for detection and identification ofF. tularensis.Method:For performing this research, the complete genomes ofF. tularensissubsp.tularensisFSC198,F. tularensissubsp.holarcticaLVS,F. tularensissubsp.mediasiatica,F. tularensissubsp.novicida(F. novicidaU112), andF. philomiragiasubsp.philomiragiaATCC 25017 were studiedviaNCBI BLAST tool, GView and PanSeq Servers and finally the microarray probes were produced and processedviaAlleleID 7.7 software and Oligoanalyzer tool, respectively.Results:In thisin silicoinvestigation, a number of long oligo microarray probes were designed for detecting and identifyingF. tularensis. Among these probes, 15 probes were recognized as the best candidates for microarray chip designing.Conclusion:Calibrated microarray probes reduce the biasis of DNA microarray technology as an advanced, rapid, accurate and cost-effective molecular diagnostic tool with high specificity and sensitivity. Professional microarray probe designing provides us with much more facility and flexibility regarding preparation of a microarray diagnostic chip.

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