Flow Cytometric Assay for Genotyping Cytochrome P450 2C9 and 2C19

Pickering, Jerry W.; McMillin, Gwendolyn A.; Gedge, Friederike; Hill, Harry R.; Lyon, Elaine

doi:10.2165/00129785-200404030-00007

Cited by 23 publications

(12 citation statements)

References 24 publications

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“…Molecular assays utilizing this technology and instrumentation and targeting other genetic markers of human disease have previously been licensed by the FDA (1,11,13,21,27).…”

Section: Discussionmentioning

confidence: 99%

Comparison of the GenMark Diagnostics eSensor Respiratory Viral Panel to Real-Time PCR for Detection of Respiratory Viruses in Children

Pierce

Hodinka

2012

J Clin Microbiol

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A novel eSensor respiratory viral panel (eSensor RVP) multiplexed nucleic acid amplification test (GenMark Diagnostics, Inc., Carlsbad, CA) was compared to laboratory-developed real-time PCR assays for the detection of various respiratory viruses. A total of 250 frozen archived pediatric respiratory specimens previously characterized as either negative or positive for one or more viruses by real-time PCR were examined using the eSensor RVP. Overall agreement between the eSensor RVP and corresponding real-time PCR assays for shared analytes was 99.2% (kappa ‫؍‬ 0.96 [95% confidence interval {CI}, 0.94 to 0.98]). The combined positive percent agreement was 95.4% (95% CI, 92.5 to 97.3); the negative percent agreement was 99.7% (95% CI, 99.4 to 99.8). The mean real-time PCR threshold cycle (C T ) value for specimens with discordant results was 39.73 (95% CI, 38.03 to 41.43). Detection of coinfections and correct identification of influenza A virus subtypes were comparable between methods. Of note, the eSensor RVP rhinovirus assay was found to be more sensitive and specific than the corresponding rhinovirus real-time PCR. In contrast, the eSensor RVP adenovirus B, C, and E assays demonstrated some cross-reactivity when tested against known adenovirus serotypes representing groups A through F. The eSensor RVP is robust and relatively easy to perform, it involves a unique biosensor technology for target detection, and its multiplexed design allows for efficient and simultaneous interrogation of a single specimen for multiple viruses. Potential drawbacks include a slower turnaround time and the need to manipulate amplified product during the protocol, increasing the possibility of contamination.A cute viral upper and lower respiratory tract infections are responsible for substantial morbidity in both pediatric and adult populations worldwide. These infections can be severe and even fatal, especially in susceptible infants, older adults, patients with compromised immune systems, and individuals with underlying cardiopulmonary diseases. Rapid and accurate laboratory detection of respiratory viruses plays an important role in clinical management, guiding the appropriate prescription of antivirals, reducing the need for additional diagnostic studies and hospital procedures, and limiting the use of unnecessary antibiotics (2,4,5,6,10,19,31,35). In addition, a virologic diagnosis is instrumental to efforts focused on prevention of health care-associated infections (3,9,23,24).PCR has demonstrated superior sensitivity for the detection of respiratory viruses over the more conventional laboratory methods of virus culture and rapid direct antigen detection tests (7,12,20,22,34). Both laboratory-developed and commercial molecular assays are now available, but the overall complexity of most of these tests has made implementation challenging for many clinical laboratories (18). However, significant recent advances in microfluidics, microelectronics, and microfabrication have allowed the development of simplified molecular systems t...

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“…Molecular assays utilizing this technology and instrumentation and targeting other genetic markers of human disease have previously been licensed by the FDA (1,11,13,21,27).…”

Section: Discussionmentioning

confidence: 99%

Comparison of the GenMark Diagnostics eSensor Respiratory Viral Panel to Real-Time PCR for Detection of Respiratory Viruses in Children

Pierce

Hodinka

2012

J Clin Microbiol

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“…Using this assay, we also determined CYP2B6 allele and genotype frequencies in Asian, Caucasian, Hispanic, and African individuals from North America to compare with previous findings. Recently, a similar assay has been used for analyzing the most common mutant alleles of CYP2C9 and CYP2C19 [32].…”

Section: Introductionmentioning

confidence: 99%

Prevalence of CYP2B6 alleles in malaria-endemic populations of West Africa and Papua New Guinea

Mehlotra

Ziats

Bockarie

et al. 2006

Eur J Clin Pharmacol

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Objective-Cytochrome P450 2B6 (CYP2B6) is involved in the metabolism of artemisinin drugs, a novel series of antimalarials. Our aim was to analyze the prevalence of the most commonly observed CYP2B6 alleles in malaria-endemic populations of West Africa (WA) and Papua New Guinea (PNG).Methods-Using a post-PCR ligation detection reaction-fluorescent microsphere assay, frequencies of CYP2B6*1A, *2, *3, *4, *5, *6, *7, and *9 were determined in WA (n=166) and PNG (n=174). To compare with the results of previous studies, we also determined the allele frequencies in 291 North Americans of various ethnic groups.Results-Significant differences were observed between WA and PNG for the frequencies of alleles CYP2B6*1A (45% vs 33%, P = 0.003), *2 (4% vs. 0%, P<0.001), *6 (42% vs 62%, P<0.001), and *9 (8% vs 1%, P<0.001), and genotypes *1A/*9 (9% vs 0%, P<0.001) and *6/*6 (17% vs 43%, P<0.001). The frequencies of CYP2B6 genotypes in the populations were in HardyWeinberg equilibrium, except for PNG where an overall significant deficit of heterozygosity was observed (H O =0.431, H E =0.505, P=0.004). The allele frequencies in Asian-Americans and Caucasians-Americans were comparable to those documented for Japanese and Caucasian populations.Conclusions-CYP2B6 variants, previously shown to affect metabolism of a variety of drugs, occur in WA and PNG, and there are significant genetic differences at the CYP2B6 locus in these populations. It may be important to determine if these differences alter the efficacy of artemisinin drugs.

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“…This parameter depends on the identity of the microsphere and related chemistry reactions performed to couple the probe to the surface. Microspheres developed from a range of materials have been reported as suitable for gene expression studies, but the most common are polystyrene (Carson and Vignali 1999; Ye et al 2001; Bortolin et al 2004; Fuja et al 2004; Martins et al 2004; Pickering et al 2004) and silica (Battersby et al 2002; Kuhn et al 2004). The surface of these microspheres is typically carboxylated to enable the covalent attachment of oligonucleotide probes.…”

Section: Resultsmentioning

confidence: 99%

“…As microsphere-based probes are randomly located in a suspension in a very small volume (unlike the compounds in microarrays and microplates which are in a fixed, known, position on an array), an encoding system is required to allow the rapid identification of the probe structures or reconstruction of the target sequences. Recent reports have described the application of multiplexed, microsphere-based assays in polymorphism genotyping (Ye et al 2001; Xu et al 2003; Bortolin et al 2004; Pickering et al 2004) and gene expression profiling (Fuja et al 2004; Kuhn et al 2004). …”

Section: Introductionmentioning

confidence: 99%

Multiplexed microsphere diagnostic tools in gene expression applications: factors and futures

Lawrie¹,

Robinson²,

Corrie³

et al. 2006

International Journal of Nanomedicine

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Abstract:Microarrays have received significant attention in recent years as scientists have firstly identified factors that can produce reduced confidence in gene expression data obtained on these platforms, and secondly sought to establish laboratory practices and a set of standards by which data are reported with integrity. Microsphere-based assays represent a new generation of diagnostics in this field capable of providing substantial quantitative and qualitative information from gene expression profiling. However, for gene expression profiling, this type of platform is still in the demonstration phase, with issues arising from comparative studies in the literature not yet identified. It is desirable to identify potential parameters that are established as important in controlling the information derived from microsphere-based hybridizations to quantify gene expression. As these evolve, a standard set of parameters will be established that are required to be provided when data are submitted for publication. Here we initiate this process by identifying a number of parameters we have found to be important in microsphere-based assays designed for the quantification of low abundant genes which are variable between studies.

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Flow Cytometric Assay for Genotyping Cytochrome P450 2C9 and 2C19

Abstract: Both the in-house Luminex method and the eSensor trade mark DNA detection system reproducibly and unambiguously genotyped SNPs of CYP2C9 and CYP2C19 in the samples tested.

Cited by 23 publications

References 24 publications

Comparison of the GenMark Diagnostics eSensor Respiratory Viral Panel to Real-Time PCR for Detection of Respiratory Viruses in Children

Comparison of the GenMark Diagnostics eSensor Respiratory Viral Panel to Real-Time PCR for Detection of Respiratory Viruses in Children

Prevalence of CYP2B6 alleles in malaria-endemic populations of West Africa and Papua New Guinea

Multiplexed microsphere diagnostic tools in gene expression applications: factors and futures

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