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1.
JAMA Netw Open ; 4(11): e2129647, 2021 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-34724555

RESUMEN

Importance: Randomized clinical trials in prostate cancer have reported noninferior outcomes for hypofractionated radiation therapy (HRT) compared with conventional RT (CRT); however, uptake of HRT across jurisdictions is variable. Objective: To evaluate the use of HRT vs CRT in men with nonmetastatic prostate cancer and compare patient-reported outcomes (PROs) at a population level. Design, Setting, and Participants: Registry-based cohort study from the Australian and New Zealand Prostate Cancer Outcomes Registry (PCOR-ANZ). Participants were men with nonmetastatic prostate cancer treated with primary RT (excluding brachytherapy) from January 2016 to December 2019. Data were analyzed in March 2021. Exposures: HRT defined as 2.5 to 3.3 Gy and CRT defined as 1.7 to 2.3 Gy per fraction. Main Outcomes and Measures: Temporal trends and institutional, clinicopathological, and sociodemographic factors associated with use of HRT were analyzed. PROs were assessed 12 months following RT using the Expanded Prostate Cancer Index Composite (EPIC)-26 Short Form questionnaire. Differences in PROs were analyzed by adjusting for age and National Comprehensive Cancer Network risk category. Results: Of 8305 men identified as receiving primary RT, 6368 met the inclusion criteria for CRT (n = 4482) and HRT (n = 1886). The median age was 73.1 years (IQR, 68.2-77.3 years), 2.6% (168) had low risk, 45.7% (2911) had intermediate risk, 44.5% (2836) had high-/very high-risk, and 7.1% (453) had regional nodal disease. Use of HRT increased from 2.1% (9 of 435) in the first half of 2016 to 52.7% (539 of 1023) in the second half of 2019, with lower uptake in the high-/very high-risk (1.9% [4 of 215] to 42.4% [181 of 427]) compared with the intermediate-risk group (2.2% [4 of 185] to 67.6% [325 of 481]) (odds ratio, 0.26; 95% CI, 0.15-0.45). Substantial variability in the use of HRT for intermediate-risk disease remained at the institutional level (median 53.3%; range, 0%-100%) and clinician level (median 57.9%; range, 0%-100%) in the last 2 years of the study period. There were no clinically significant differences across EPIC-26 urinary and bowel functional domains or bother scores. Conclusions and Relevance: In this cohort study, use of HRT for prostate cancer increased substantially from 2016. This population-level data demonstrated clinically equivalent PROs and supports the continued implementation of HRT into routine practice. The wide variation in practice observed at the jurisdictional, institutional, and clinician level provides stakeholders with information that may be useful in targeting implementation strategies and benchmarking services.


Asunto(s)
Satisfacción del Paciente , Neoplasias de la Próstata/psicología , Neoplasias de la Próstata/radioterapia , Anciano , Anciano de 80 o más Años , Australia , Estudios de Cohortes , Fraccionamiento de la Dosis de Radiación , Humanos , Masculino , Nueva Zelanda , Medición de Resultados Informados por el Paciente , Satisfacción del Paciente/estadística & datos numéricos , Sistema de Registros , Resultado del Tratamiento
2.
Nat Commun ; 8: 14049, 2017 01 16.
Artículo en Inglés | MEDLINE | ID: mdl-28091601

RESUMEN

Characterizing the transcriptome of individual cells is fundamental to understanding complex biological systems. We describe a droplet-based system that enables 3' mRNA counting of tens of thousands of single cells per sample. Cell encapsulation, of up to 8 samples at a time, takes place in ∼6 min, with ∼50% cell capture efficiency. To demonstrate the system's technical performance, we collected transcriptome data from ∼250k single cells across 29 samples. We validated the sensitivity of the system and its ability to detect rare populations using cell lines and synthetic RNAs. We profiled 68k peripheral blood mononuclear cells to demonstrate the system's ability to characterize large immune populations. Finally, we used sequence variation in the transcriptome data to determine host and donor chimerism at single-cell resolution from bone marrow mononuclear cells isolated from transplant patients.


Asunto(s)
Leucocitos Mononucleares/metabolismo , Transcriptoma , Línea Celular , Femenino , Humanos , Leucocitos Mononucleares/química , Masculino , ARN Mensajero/genética , ARN Mensajero/metabolismo , Análisis de la Célula Individual
3.
J Med Radiat Sci ; 63(3): 161-9, 2016 09.
Artículo en Inglés | MEDLINE | ID: mdl-27648280

RESUMEN

INTRODUCTION: The aim of the study is to review the long-term oncological outcomes and adverse effects of post-operative radiotherapy (PORT) for Stage I/II seminoma patients in an Australian radiation treatment centre. METHODS: This is a retrospective study of 125 patients with Stage I/II seminoma treated with PORT at the Alfred Health Radiation Oncology Service between 1992 and 2013. Patients were linked to the Victorian Cancer Registry to enable confirmation of survival and diagnosis of secondary malignancies (SM). The relapse-free survival (RFS), testicular-cancer-specific survival (TCSS), overall survival (OS) and SM-free survival (SMFS) were estimated with Kaplan-Meier methods. RESULTS: The median age at diagnosis was 36 (range 20-62). The median time between diagnosis and PORT was 1.6 months (range: 0.5-4.5). Fifty patients (40%) had PORT to the para-aortic (PA) target alone, while the remaining had PORT to PA and ipsilateral or bilateral iliac lymph nodes. There were no acute adverse effects requiring admission. The median follow-up after PORT was 7.8 years (range = 0.1-19.1). There were two relapses, both of which occurred within 1 year of PORT (estimated 10-year RFS = 98.4%). Five deaths were reported, none of which were testicular cancer-related death (estimated 10-year TCSS = 100%, 10-year OS = 97.3%). There were seven SM (one lower lip cancer, one upper shoulder melanoma, one mesothelioma, two prostate cancer, one acute myeloid leukaemia and one contralateral testicular seminoma) reported in six patients, with estimated 10-year SMFS of 92.9%. CONCLUSION: Our series confirms excellent oncological outcomes among patients with Stage I/II seminoma treated with PORT, with uncommon occurrence of SM.


Asunto(s)
Neoplasias Primarias Secundarias/etiología , Radioterapia/efectos adversos , Seminoma/radioterapia , Neoplasias Testiculares/radioterapia , Adulto , Humanos , Masculino , Persona de Mediana Edad , Periodo Posoperatorio , Seminoma/patología , Seminoma/cirugía , Neoplasias Testiculares/patología , Neoplasias Testiculares/cirugía , Resultado del Tratamiento
4.
Radiother Oncol ; 112(1): 72-6, 2014 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-25086852

RESUMEN

BACKGROUND AND PURPOSE: Erectile function (EF) is commonly affected following prostate cancer treatment. We aim to evaluate the long-term EF following seed brachytherapy (BT) treatment. MATERIALS AND METHODS: The study consisted of 366 patients treated with BT at our institution, who completed the IIEF-5 questionnaire and reported no or mild erectile dysfunction (ED) pre-BT. The probability of EF preservation post-BT was estimated using the Kaplan-Meier methods. The difference in EF preservation by patient-, tumour- and treatment-related factors was assessed using the log-rank test. Multivariate Cox regression was used to estimate the effect of each factor on EF preservation. RESULTS: Of the 366 patients, 277 (76%) reported normal EF, and 89 (24%) reported mild ED. The patients were followed-up for a median of 41 months (range: 3-124), and the 5-year actuarial rate of EF preservation was 59%. Age at BT seed implant, presence of medical comorbidities, Gleason score and the biologically effective dose (BED) are associated with EF preservation (P < 0.005). The association for these four factors remains statistically significant in multivariate analysis, with Gleason score having the strongest effect (HR = 3.7; 95% CI = 2.6-5.4). CONCLUSION: The 5-year actuarial rate of EF preservation post-BT in our cohort is 59%, and is influenced by multiple factors.


Asunto(s)
Braquiterapia/efectos adversos , Disfunción Eréctil/etiología , Neoplasias de la Próstata/radioterapia , Traumatismos por Radiación/etiología , Adulto , Anciano , Anciano de 80 o más Años , Estudios de Cohortes , Disfunción Eréctil/tratamiento farmacológico , Humanos , Masculino , Persona de Mediana Edad , Análisis Multivariante , Erección Peniana/fisiología , Erección Peniana/efectos de la radiación , Inhibidores de Fosfodiesterasa 5/uso terapéutico , Modelos de Riesgos Proporcionales , Neoplasias de la Próstata/patología , Estudios Retrospectivos , Índice de Severidad de la Enfermedad , Encuestas y Cuestionarios
5.
Anal Chem ; 85(23): 11619-27, 2013 Dec 03.
Artículo en Inglés | MEDLINE | ID: mdl-24180464

RESUMEN

Two years ago, we described the first droplet digital PCR (ddPCR) system aimed at empowering all researchers with a tool that removes the substantial uncertainties associated with using the analogue standard, quantitative real-time PCR (qPCR). This system enabled TaqMan hydrolysis probe-based assays for the absolute quantification of nucleic acids. Due to significant advancements in droplet chemistry and buoyed by the multiple benefits associated with dye-based target detection, we have created a "second generation" ddPCR system compatible with both TaqMan-probe and DNA-binding dye detection chemistries. Herein, we describe the operating characteristics of DNA-binding dye based ddPCR and offer a side-by-side comparison to TaqMan probe detection. By partitioning each sample prior to thermal cycling, we demonstrate that it is now possible to use a DNA-binding dye for the quantification of multiple target species from a single reaction. The increased resolution associated with partitioning also made it possible to visualize and account for signals arising from nonspecific amplification products. We expect that the ability to combine the precision of ddPCR with both DNA-binding dye and TaqMan probe detection chemistries will further enable the research community to answer complex and diverse genetic questions.


Asunto(s)
ADN/análisis , Colorantes Fluorescentes/química , Reacción en Cadena de la Polimerasa Multiplex/métodos , ADN/metabolismo , Colorantes Fluorescentes/metabolismo , Humanos , Unión Proteica/fisiología , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos
6.
Nat Methods ; 10(10): 1003-5, 2013 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-23995387

RESUMEN

Nanoliter-sized droplet technology paired with digital PCR (ddPCR) holds promise for highly precise, absolute nucleic acid quantification. Our comparison of microRNA quantification by ddPCR and real-time PCR revealed greater precision (coefficients of variation decreased 37-86%) and improved day-to-day reproducibility (by a factor of seven) of ddPCR but with comparable sensitivity. When we applied ddPCR to serum microRNA biomarker analysis, this translated to superior diagnostic performance for identifying individuals with cancer.


Asunto(s)
Biomarcadores de Tumor/análisis , MicroARNs/análisis , Reacción en Cadena en Tiempo Real de la Polimerasa/métodos , Biomarcadores de Tumor/sangre , Humanos , Límite de Detección , Masculino , MicroARNs/sangre , Neoplasias de la Próstata/sangre , Neoplasias de la Próstata/diagnóstico , Reacción en Cadena en Tiempo Real de la Polimerasa/normas , Reproducibilidad de los Resultados , Sensibilidad y Especificidad
7.
Clin Chem ; 59(6): 991-4, 2013 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-23358413

RESUMEN

BACKGROUND: Human epidermal growth factor receptor 2 (HER2) testing is routinely performed by immunohistochemistry (IHC) and/or fluorescence in situ hybridization (FISH) analyses for all new cases of invasive breast carcinoma. IHC is easier to perform, but analysis can be subjective and variable. FISH offers better diagnostic accuracy and added confidence, particularly when it is used to supplement weak IHC signals, but it is more labor intensive and costly than IHC. We examined the performance of droplet digital PCR (ddPCR) as a more precise and less subjective alternative for quantifying HER2 DNA amplification. METHODS: Thirty-nine cases of invasive breast carcinoma containing ≥30% tumor were classified as positive or negative for HER2 by IHC, FISH, or both. DNA templates for these cases were prepared from formalin-fixed paraffin-embedded (FFPE) tissues to determine the HER2 copy number by ddPCR. ddPCR involved emulsifying hydrolysis probe-based PCR reaction mixtures containing the ERBB2 [v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian); also known as HER2] gene and chromosome 17 centromere assays into nanoliter-sized droplets for thermal cycling and analysis. RESULTS: ddPCR distinguished, through differences in the level of HER2 amplification, the 10 HER2-positive samples from the 29 HER2-negative samples with 100% concordance to HER2 status obtained by FISH and IHC analysis. ddPCR results agreed with the FISH results for the 6 cases that were equivocal by IHC analyses, confirming 2 of these samples as positive for HER2 and the other 4 as negative. CONCLUSIONS: ddPCR can be used as a molecular-analysis tool to precisely measure copy number alterations in FFPE samples of heterogeneous breast tumor tissue.


Asunto(s)
Neoplasias de la Mama/genética , Dosificación de Gen , Técnicas Genéticas/normas , Reacción en Cadena de la Polimerasa/normas , Receptor ErbB-2/genética , Computadores , Femenino , Formaldehído/química , Humanos , Adhesión en Parafina , Reproducibilidad de los Resultados
8.
Brachytherapy ; 12(1): 50-5, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-22561217

RESUMEN

PURPOSE: High-dose-rate brachytherapy is an established technique to deliver a conformal dose of radiation to patients with prostate cancer. The William Buckland Radiotherapy Center has been performing high-dose-rate brachytherapy with external beam radiation treatment for prostate cancer since 1998 and has an extensive prospective database on all patients treated. The purpose of this analysis was to assess the risk of stricture formation and identify the predictive or causative factors. METHODS AND MATERIALS: Three hundred fifty-four patients were treated between 1998 and 2008. Patients received one of three differing dose schedules: 20Gy in four treatments (20Gy/4), 18Gy/3, and 19Gy/2 during three sequential time periods. Nelson-Aalen cumulative hazard modeling was used to estimate risk of events over time. Potential risk factors, including dose, were identified and used in the analysis. RESULTS: There were 45 patients who developed at least one stricture, an overall risk of 8.2% at 2 years. The 2-year risk of stricture formation was 3.4%, 2.3%, and 31.6% for 18Gy/3, 20Gy/4, and 19Gy/2, respectively. Most strictures occurred in the bulbomembranous urethra (50%) or external sphincter region (33%). On multivariable analysis, the dose schedule used was the only significant predictor for increased stricture formation. CONCLUSIONS: In our patients, those who received 19Gy/2 were at a significantly higher risk of stricture formation. Most of these strictures were mild, requiring only one intervention but a 2-year stricture risk of 31.6% was striking, and we have modified our protocol.


Asunto(s)
Braquiterapia/estadística & datos numéricos , Neoplasias de la Próstata/epidemiología , Neoplasias de la Próstata/radioterapia , Traumatismos por Radiación/epidemiología , Estrechez Uretral/epidemiología , Anciano , Anciano de 80 o más Años , Comorbilidad , Humanos , Incidencia , Masculino , Persona de Mediana Edad , Radioterapia , Medición de Riesgo , Resultado del Tratamiento , Victoria/epidemiología
9.
Methods ; 59(1): S20-3, 2013 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-23036330

RESUMEN

UNLABELLED: The human epidermal growth factor receptor 2 (HER2, also known as erbB2) gene is involved in signal transduction for cell growth and differentiation. It is a cell surface receptor tyrosine kinase and a proto-oncogene. Overexpression of HER2 is of clinical relevance in breast cancer due to its prognostic value correlating elevated expression with worsening clinical outcome. At the same time, HER2 assessment is also of importance because successful anti-tumor treatment with Herceptin® is strongly correlated with HER2 overexpression in the tumor (approximately 30% of all breast tumors overexpress HER2). In a comprehensive national study, Wolff et al. [1] state that "Approximately 20% of current HER2 testing may be inaccurate" which underscores the importance of developing more accurate methods to determine HER2 status. Droplet Digital™ PCR (ddPCR™) has the potential to improve upon HER2 measurements due to its ability to quantitate DNA and RNA targets with high precision and accuracy. Here we present a study which investigates whether ddPCR can be used to assess HER2 transcript levels in formalin-fixed paraffin embedded (FFPE) human breast tumors and whether these ddPCR measurements agree with prior assessments of these same samples by pathologists using immunohistochemistry (IHC) and in some cases fluorescence in situ hybridization (FISH). We also determined the copy number of HER2 in these samples as compared to the CEP17 reference gene. RESULTS: Clinical FFPE samples were successfully studied using ddPCR and compared to results from standard FISH and IHC methodology. The results demonstrate that ddPCR can rank order the samples in complete agreement with the current standard methods and that ddPCR has the added benefit of providing quantitative results, rather than relying on the expert skill of a seasoned pathologist for determination.


Asunto(s)
Neoplasias de la Mama/metabolismo , Expresión Génica , Técnicas de Diagnóstico Molecular/normas , Reacción en Cadena de la Polimerasa/normas , Receptor ErbB-2/genética , Centrómero/genética , Femenino , Fijadores/química , Formaldehído/química , Dosificación de Gen , Humanos , Inmunohistoquímica , Hibridación Fluorescente in Situ , Adhesión en Parafina , Proto-Oncogenes Mas , ARN Mensajero/genética , ARN Mensajero/metabolismo , Receptor ErbB-2/metabolismo , Estándares de Referencia
10.
J Med Imaging Radiat Oncol ; 56(1): 18-30, 2012 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-22339742

RESUMEN

Curative radiotherapy, with or without concurrent chemotherapy, is recognized as a standard treatment option for muscle-invasive bladder cancer. It is commonly used for two distinct groups of patients: either for those medically unfit for surgery, or as part of a 'bladder preserving' management plan incorporating the possibility of salvage cystectomy. However, in both situations, the approach to radiotherapy varies widely around the world. The Australian and New Zealand Faculty of Radiation Oncology Genito-Urinary Group recognised a need to develop consistent, evidence-based guidelines for patient selection and radiotherapy technique in the delivery of curative radiotherapy. Following a workshop convened in May 2009, a working party collated opinions and conducted a wide literature appraisal linking each recommendation with the best available evidence. This process was subject to ongoing re-presentation to the Faculty of Radiation Oncology Genito-Urinary Group members prior to final endorsement. These Guidelines include patient selection, radiation target delineation, dose and fractionation schedules, normal tissue constraints and investigational techniques. Particular emphasis is given to the rationale for the target volumes described. These Guidelines provide a consensus-based framework for the delivery of curative radiotherapy for muscle-invasive bladder cancer. Widespread input from radiation oncologists treating bladder cancer ensures that these techniques are feasible in practice. We recommend these Guidelines be adopted widely in order to encourage a uniformly high standard of radiotherapy in this setting, and to allow for better comparison of outcomes.


Asunto(s)
Oncología por Radiación/normas , Neoplasias de la Vejiga Urinaria/radioterapia , Australia , Medicina Basada en la Evidencia , Humanos , Invasividad Neoplásica , Nueva Zelanda , Neoplasias de la Vejiga Urinaria/patología , Urotelio/patología , Urotelio/efectos de la radiación
11.
Anal Chem ; 84(2): 1003-11, 2012 Jan 17.
Artículo en Inglés | MEDLINE | ID: mdl-22122760

RESUMEN

Droplet digital polymerase chain reaction (ddPCR) is a new technology that was recently commercialized to enable the precise quantification of target nucleic acids in a sample. ddPCR measures absolute quantities by counting nucleic acid molecules encapsulated in discrete, volumetrically defined, water-in-oil droplet partitions. This novel ddPCR format offers a simple workflow capable of generating highly stable partitioning of DNA molecules. In this study, we assessed key performance parameters of the ddPCR system. A linear ddPCR response to DNA concentration was obtained from 0.16% through to 99.6% saturation in a 20,000 droplet assay corresponding to more than 4 orders of magnitude of target DNA copy number per ddPCR. Analysis of simplex and duplex assays targeting two distinct loci in the Lambda DNA genome using the ddPCR platform agreed, within their expanded uncertainties, with values obtained using a lower density microfluidic chamber based digital PCR (cdPCR). A relative expanded uncertainty under 5% was achieved for copy number concentration using ddPCR. This level of uncertainty is much lower than values typically observed for quantification of specific DNA target sequences using currently commercially available real-time and digital cdPCR technologies.


Asunto(s)
Bacteriófago lambda/genética , Variaciones en el Número de Copia de ADN , ADN/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Reacción en Cadena de la Polimerasa , Genoma
12.
Anal Chem ; 83(22): 8604-10, 2011 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-22035192

RESUMEN

Digital PCR enables the absolute quantitation of nucleic acids in a sample. The lack of scalable and practical technologies for digital PCR implementation has hampered the widespread adoption of this inherently powerful technique. Here we describe a high-throughput droplet digital PCR (ddPCR) system that enables processing of ~2 million PCR reactions using conventional TaqMan assays with a 96-well plate workflow. Three applications demonstrate that the massive partitioning afforded by our ddPCR system provides orders of magnitude more precision and sensitivity than real-time PCR. First, we show the accurate measurement of germline copy number variation. Second, for rare alleles, we show sensitive detection of mutant DNA in a 100,000-fold excess of wildtype background. Third, we demonstrate absolute quantitation of circulating fetal and maternal DNA from cell-free plasma. We anticipate this ddPCR system will allow researchers to explore complex genetic landscapes, discover and validate new disease associations, and define a new era of molecular diagnostics.


Asunto(s)
ADN/genética , Dosificación de Gen/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Reacción en Cadena de la Polimerasa , Humanos
13.
J Vet Diagn Invest ; 21(6): 760-70, 2009 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-19901276

RESUMEN

Bluetongue virus (BTV) causes disease in domestic and wild ruminants and results in significant economic loss. The closely related Epizootic hemorrhagic disease virus (EHDV) has been associated with bluetongue-like disease in cattle. Although U.S. EHDV strains have not been experimentally proven to cause disease in cattle, there is serologic evidence of infection in cattle. Therefore, rapid diagnosis and differentiation of BTV and EHDV is required. The genetic sequence information and bioinformatic analysis necessary to design a real-time reverse transcription polymerase chain reaction (RT-PCR) assay for the early detection of indigenous and exotic BTV and EHDV is described. This sequence data foundation focused on 2 conserved target genes: one that is highly expressed in infected mammalian cells, and the other is highly expressed in infected insect cells. The analysis of all BTV and EHDV prototype strains indicated that a complex primer design was necessary for both a virus group-comprehensive and virus group-specific gene amplification diagnostic test. This information has been used as the basis for the development of a rapid multiplex BTV-EHDV real-time RT-PCR that detects all known serotypes of both viruses and distinguishes between BTV and EHDV serogroups. The sensitivity of this rapid, single-tube, real-time RT-PCR assay is sufficient for diagnostic application, without the contamination problems associated with standard gel-based RT-PCR, especially nested RT-PCR tests.


Asunto(s)
Virus de la Lengua Azul/genética , Virus de la Enfermedad Hemorrágica Epizoótica/genética , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/métodos , Animales , Secuencia de Bases , Lengua Azul/epidemiología , Virus de la Lengua Azul/clasificación , Bovinos , Enfermedades de los Bovinos/epidemiología , Enfermedades de los Bovinos/virología , Clonación Molecular , Cartilla de ADN , Amplificación de Genes , Virus de la Enfermedad Hemorrágica Epizoótica/clasificación , Filogenia , Infecciones por Reoviridae/epidemiología , Serotipificación , Especificidad de la Especie
14.
Anal Chem ; 80(19): 7422-9, 2008 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-18763806

RESUMEN

We have developed and field-tested a now operational civilian biodefense capability that continuously monitors the air in high-risk locations for biological threat agents. This stand-alone instrument, called the Autonomous Pathogen Detection System (APDS), collects and selectively concentrates particles from the air into liquid samples and analyzes the samples using multiplexed PCR amplification coupled with microsphere array detection. During laboratory testing, we evaluated the APDS instrument's response to Bacillus anthracis and Yersinia pestis by spiking the liquid sample stream with viable spores and cells, bead-beaten lysates, and purified DNA extracts. APDS results were also compared to a manual real-time PCR method. Field data acquired during 74 days of continuous operation at a mass-transit subway station are presented to demonstrate the specificity and reliability of the APDS. The U.S. Department of Homeland Security recently selected the APDS reported herein as the first autonomous detector component of their BioWatch antiterrorism program. This sophisticated field-deployed surveillance capability now generates actionable data in one-tenth the time of manual filter collection and analysis.


Asunto(s)
Bacillus anthracis/aislamiento & purificación , Monitoreo del Ambiente/métodos , Reacción en Cadena de la Polimerasa/métodos , Yersinia pestis/aislamiento & purificación , Bioterrorismo , Monitoreo del Ambiente/instrumentación , Reacción en Cadena de la Polimerasa/instrumentación
15.
J Virol Methods ; 153(1): 61-9, 2008 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-18634827

RESUMEN

A nucleic acid-based multiplexed assay was developed that combines detection of foot-and-mouth disease virus (FMDV) with rule-out assays for two other foreign animal diseases and four domestic animal diseases that cause vesicular or ulcerative lesions indistinguishable from FMDV infection in cattle, sheep and swine. The FMDV "look-alike" diagnostic assay panel contains 5 PCR and 12 reverse transcriptase PCR (RT-PCR) signatures for a total of 17 simultaneous PCR amplifications for 7 diseases plus incorporating 4 internal assay controls. It was developed and optimized to amplify both DNA and RNA viruses simultaneously in a single tube and employs Luminex liquid array technology. Assay development including selection of appropriate controls, a comparison of signature performance in single and multiplex testing against target nucleic acids, as well of limits of detection for each of the individual signatures is presented. While this assay is a prototype and by no means a comprehensive test for FMDV "look-alike" viruses, an assay of this type is envisioned to have benefit to a laboratory network in routine surveillance and possibly for post-outbreak proof of freedom from foot-and-mouth disease.


Asunto(s)
Enfermedades de los Bovinos/virología , Fiebre Aftosa/diagnóstico , Reacción en Cadena de la Polimerasa/métodos , Enfermedades de las Ovejas/virología , Enfermedades de los Porcinos/virología , Animales , Bovinos , Cartilla de ADN , Virus de la Fiebre Aftosa/genética , Virus de la Fiebre Aftosa/aislamiento & purificación , Reacción en Cadena de la Polimerasa/normas , Estándares de Referencia , Sensibilidad y Especificidad , Ovinos , Porcinos
16.
J Clin Microbiol ; 46(3): 1081-9, 2008 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-18216216

RESUMEN

A high-throughput multiplexed assay was developed for the differential laboratory detection of foot-and-mouth disease virus (FMDV) from viruses that cause clinically similar diseases of livestock. This assay simultaneously screens for five RNA and two DNA viruses by using multiplexed reverse transcription-PCR (mRT-PCR) amplification coupled with a microsphere hybridization array and flow-cytometric detection. Two of the 17 primer-probe sets included in this multiplex assay were adopted from previously characterized real-time RT-PCR (rRT-PCR) assays for FMDV. The diagnostic accuracy of the mRT-PCR assay was evaluated using 287 field samples, including 247 samples (213 true-positive samples and 35 true-negative samples) from suspected cases of foot-and-mouth disease collected from 65 countries between 1965 and 2006 and 39 true-negative samples collected from healthy animals. The mRT-PCR assay results were compared to those of two singleplex rRT-PCR assays, using virus isolation with antigen enzyme-linked immunosorbent assays as the reference method. The diagnostic sensitivity of the mRT-PCR assay for FMDV was 93.9% (95% confidence interval [CI], 89.8 to 96.4%), and the sensitivity was 98.1% (95% CI, 95.3 to 99.3%) for the two singleplex rRT-PCR assays used in combination. In addition, the assay could reliably differentiate between FMDV and other vesicular viruses, such as swine vesicular disease virus and vesicular exanthema of swine virus. Interestingly, the mRT-PCR detected parapoxvirus (n = 2) and bovine viral diarrhea virus (n = 2) in clinical samples, demonstrating the screening potential of this mRT-PCR assay to identify viruses in FMDV-negative material not previously recognized by using focused single-target rRT-PCR assays.


Asunto(s)
Enfermedades de los Bovinos/diagnóstico , Virus de la Fiebre Aftosa/aislamiento & purificación , Fiebre Aftosa/diagnóstico , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa/métodos , Enfermedades de los Porcinos/diagnóstico , Animales , Diarrea Mucosa Bovina Viral/diagnóstico , Diarrea Mucosa Bovina Viral/virología , Bovinos , Enfermedades de los Bovinos/virología , Virus de la Diarrea Viral Bovina/aislamiento & purificación , Fiebre Aftosa/virología , Virus de la Fiebre Aftosa/genética , Microesferas , Parapoxvirus/aislamiento & purificación , Infecciones por Poxviridae/veterinaria , Infecciones por Poxviridae/virología , ARN Viral/análisis , ARN Viral/aislamiento & purificación , Enfermedades de los Porcinos/virología , Enfermedad Vesicular Porcina/diagnóstico , Enfermedad Vesicular Porcina/virología
17.
Analyst ; 133(2): 248-55, 2008 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-18227949

RESUMEN

We present a fully automated DNA purification module comprised of a micro-fabricated chip and sequential injection analysis system that is designed for use within autonomous instruments that continuously monitor the environment for the presence of biological threat agents. The chip has an elliptical flow channel containing a bed (3.5 x 3.5 mm) of silica-coated pillars with height, width and center-to-center spacing of 200, 15, and 30 microm, respectively, which provides a relatively large surface area (ca. 3 cm(2)) for DNA capture in the presence of chaotropic agents. We have characterized the effect of various fluidic parameters on extraction performance, including sample input volume, capture flow rate, and elution volume. The flow-through design made the pillar chip completely reusable; carryover was eliminated by flushing lines with sodium hypochlorite and deionized water between assays. A mass balance was conducted to determine the fate of input DNA not recovered in the eluent. The device was capable of purifying and recovering Bacillus anthracis genomic DNA (input masses from 0.32 to 320 pg) from spiked environmental aerosol samples, for subsequent analysis using polymerase chain reaction-based assays.


Asunto(s)
Contaminantes Atmosféricos/análisis , Bacillus anthracis/genética , ADN Bacteriano/análisis , Monitoreo del Ambiente/métodos , Aerosoles , Animales , Diseño de Equipo , Análisis de Inyección de Flujo , Humanos , Microquímica , Análisis de Secuencia por Matrices de Oligonucleótidos , Reacción en Cadena de la Polimerasa/métodos
18.
Anal Chem ; 79(22): 8471-5, 2007 Nov 15.
Artículo en Inglés | MEDLINE | ID: mdl-17929880

RESUMEN

The first lab-on-chip system for picoliter droplet generation and PCR amplification with real-time fluorescence detection has performed PCR in isolated droplets at volumes 106 smaller than commercial real-time PCR instruments. The system utilized a shearing T-junction in a silicon device to generate a stream of monodisperse picoliter droplets that were isolated from the microfluidic channel walls and each other by the oil-phase carrier. An off-chip valving system stopped the droplets on-chip, allowing them to be thermally cycled through the PCR protocol without droplet motion. With this system, a 10-pL droplet, encapsulating less than one copy of viral genomic DNA through Poisson statistics, showed real-time PCR amplification curves with a cycle threshold of approximately 18, 20 cycles earlier than commercial instruments. This combination of the established real-time PCR assay with digital microfluidics is ideal for isolating single-copy nucleic acids in a complex environment.


Asunto(s)
Reacción en Cadena de la Polimerasa/instrumentación , Reacción en Cadena de la Polimerasa/métodos , Factores de Tiempo
19.
J Vet Diagn Invest ; 19(2): 180-4, 2007 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-17402613

RESUMEN

Initial results demonstrating the feasibility of a multiplexed liquid array immunoassay for foot-and-mouth disease viral antigen detection and simultaneous serotype differentiation are presented. Serotype-specific antibodies from rabbit and guinea pig hyperimmunesera were isolated and prepared for use in a multiplexed, bead-based assay. The performance of all of the available antibodies as both capture and detector reagents was evaluated in the multiplexed system to establish a combination exhibiting the highest homotypic responses and lowest heterotypic reactions. The multiplexed assay was evaluated against inactivated cell culture supernatant samples of the same subtype as the virus used to raise the capture and detector antibodies. Distinct serotype differentiation was observed, except in the case of serotype SAT1. Subsequently, cell culture supernatant samples from a larger pool of viral subtypes were analyzed. Distinct serotype differentiation was obtained when analyzing cell culture supernatant samples from viral serotypes C, Asia, and SAT3, irrespective of the subtype. However, limitations of the current antibody pairs were realized in some inconclusive results obtained when analyzing samples from a broader range of O, A, and SAT2 subtypes. The results obtained in this initial study will be used to further optimize the assay using polyvalent or monoclonal antibodies and move toward the analysis of clinical samples.


Asunto(s)
Virus de la Fiebre Aftosa/clasificación , Virus de la Fiebre Aftosa/aislamiento & purificación , Animales , Cobayas/virología , Inmunoensayo/métodos , Conejos/virología , Serotipificación/métodos
20.
J Pharm Biomed Anal ; 43(3): 1164-8, 2007 Feb 19.
Artículo en Inglés | MEDLINE | ID: mdl-17097256

RESUMEN

This paper describes the determination of opiate alkaloids (morphine, codeine, oripavine and thebaine) in industrial process liquors using capillary zone electrophoresis with UV-absorption detection at 214 nm. A study of cyclodextrin type and concentration revealed that the addition of 30 mM hydroxypropyl-beta-cyclodextrin to the electrolyte solution (100mM Tris adjusted to pH 2.8) was suitable to resolve the four analytes of interest. Typical analysis time was 12 min and the limit of detection for each alkaloid was 2.5 x 10(-6) M. The results for the proposed methodology were in good agreement with those of a conventional HPLC procedure. Under the same conditions, short-end injection was used to reduce the effective separation length from 41.5 to 8.5 cm, which allowed the determination of morphine and thebaine in process liquors within 2.5 min.


Asunto(s)
Alcaloides/análisis , Analgésicos Opioides/análisis , Electrocromatografía Capilar , Cromatografía Líquida de Alta Presión , Codeína/análisis , Ciclodextrinas/análisis , Indicadores y Reactivos , Morfina/análisis , Solventes , Espectrofotometría Ultravioleta , Tebaína/análogos & derivados , Tebaína/análisis
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