ORCID Profile
0000-0003-0709-5164
Current Organisation
National Measurement Institute
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Publisher: Wiley
Date: 03-1990
Publisher: Springer Science and Business Media LLC
Date: 20-07-2007
Publisher: American Chemical Society (ACS)
Date: 04-08-2009
DOI: 10.1021/AC901116F
Abstract: The increased presence of 5-methycytosine at gene promoter regions may be diagnostic of cancer. However, there are many stages in the measurement of gene promoter 5-methylcytosine content where inaccuracies may occur, and this may prevent the use of these measurements for diagnostic or prognostic purposes. A high accuracy LC-MS system was developed for measuring the degree of methylation in two 100 base pair licons generated by the polymerase chain reaction (PCR) and in which 5-methylcytidine had been synthetically incorporated. Nucleotide monophosphate reference materials were used to calibrate the peak area ratio of cytidine and 5-methylcytidine to their mole ratio in enzymatic hydrolysates of the licons, thus enabling metrological traceability of the methylation ratio to the mole. The methylation values obtained agreed closely with the reference values assigned to the materials. A measurement uncertainty budget was completed and showed that the moisture content of the nucleotide monophosphate reference materials was the largest source of uncertainty in the methylation ratio measurement. Measurement of an oligonucleotide supplied with the materials provided evidence that such materials may be used for calibration of DNA methylation ratios without the need for measurement of moisture content. This raises the possibility that submicrogram amounts of appropriately characterized oligonucleotide reference materials could be used to calibrate methylation ratios obtained by contemporary methodologies (such as PCR after bisulfite conversion of genomic DNA) yielding values that are traceable to the International System of Units (SI). Such calibrated gene methylation measurements would then be internationally comparable as required for effective diagnostic and prognostic measurements.
Publisher: Oxford University Press (OUP)
Date: 07-2014
DOI: 10.1373/CLINCHEM.2013.219956
Abstract: DNA methylation biomarkers capable of diagnosis and subtyping have been found for many cancers. Fifteen such markers have previously been identified for pediatric acute lymphoblastic leukemia (ALL). Validation of these markers is necessary to assess their clinical utility for molecular diagnostics. Substantial efficiencies could be achieved with these DNA methylation markers for disease tracking with potential to replace patient-specific genetic testing. We evaluated DNA methylation of promoter regions of TLX3 (T-cell leukemia homeobox) and FOXE3 (forkhead box E3) in bone marrow biopsies from 197 patients classified as leukemic (n = 95) or clear of the disease (n = 102) by MALDI-TOF. Using a single nucleotide extension assay (methylSABER), we tested 10 bone marrow biopsies collected throughout the course of patient chemotherapy. Using reference materials, diagnostic thresholds and limits of detection were characterized for both methods. Reliable detection of DNA methylation of TLX3 and FOXE3 segregated ALL from those clear of disease with minimal false-negative and false-positive results. The limit of detection with MALDI-TOF was 1000–5000 copies of methylated allele. For methylSABER, the limit of detection was 10 copies of methylated TLX3, which enabled monitoring of minimal residual disease in ALL patients. Mass spectrometry procedures can be used to regionally multiplex and detect rare DNA methylation events, establish DNA methylation loci as clinically applicable biomarkers for disease diagnosis, and track pediatric ALL.
Publisher: American Chemical Society (ACS)
Date: 11-1988
DOI: 10.1021/JF00084A015
Publisher: Elsevier BV
Date: 09-2022
DOI: 10.1016/J.JMOLDX.2022.06.003
Abstract: Standardization of molecular diagnostics is fundamental for effective application of genetic analyses in personalized medicine. The amount of DNA extracted from a specimen can have a significant impact on diagnostic accuracy, especially in cases where the diagnostic variant has a low concentration such as cancer. Blood and tissue s les were supplied to genetic laboratories to assess the reproducibility of extraction methodologies DNA was extracted using participants' routine procedures and returned to the external quality assessment provider. The amount of DNA was measured by two independent analytical techniques, fluorescence intensity of intercalating dye and digital PCR DNA quality was evaluated by DNA integrity number scores. The amount of DNA extracted varied widely between and within participants and for different blood volumes, indicating that consistent diagnostic quality is challenging even within a single test center. The median digital PCR-measured amount of DNA was on average six times higher than the intercalating dye measurements obtained in this study, indicating the possibility that the latter quantitative method may significantly underestimate the amount of DNA, thus making it not fit for purpose. Standardization of genetic diagnostic tests will require a significant improvement in the reproducibility of DNA extraction this could be achieved if suppliers and users of DNA extraction kits validate their extraction methodology using reliable quantitative measurements or reference materials.
Publisher: Elsevier BV
Date: 08-1982
Publisher: Elsevier BV
Date: 03-1981
DOI: 10.1016/0009-8981(81)90348-X
Abstract: Two metabolites, 4-hydroxyisovaleric acid and mesaconic acid, have been identified and quantified in the urine of a patient with isovaleric acidemia. These compounds do not appear to have been reported previously as being components of human metabolism. In addition, large quantities of 3-methylbutyrolactone, the lactone of 4-hydroxyisovaleric acid, were observed in the volatile profile obtained by headspace chromatography. The demonstration of 4-hydroxyisovaleric acid supports the contention that urinary methylsuccinic acid seen in patients with isovaleric acidemia has arisen by omega-oxidation of isovaleric acid. The identification of mesaconic acid may indicate that the methylsuccinic acid formed in these patients is subject to further metabolism.
Publisher: Wiley
Date: 08-1978
Abstract: A quantitative method for the simultaneous determination of five anticonvulsants in serum has been developed using chemical ionization mass spectrometry without prior chromatographic separation. The technique was shown to be rapid, simple and sensitive, allowing the routine analysis of 50 microliter of serum with good within-day and day-to-day precision.
Publisher: Elsevier BV
Date: 09-1985
DOI: 10.1016/0003-2697(85)90593-7
Abstract: Fresh wheat tops were extracted with acidic 90% ethanol, and the ethanol was evaporated and a portion of the aqueous residue loaded onto DEAE-Sephadex. Organic acids were eluted with pyridinium formate and then lyophilized and the dried residue was derivatized with 1% trimethylchlorosilane in bis(trimethylsilyl)trifluoroacetamide. The acids were then quantitatively determined using capillary gas chromatography and identified using capillary gas chromatography-mass spectrometry. The acidic ethanol extraction of fresh plant tissue was quantitative for all acids except citric while losses in the remaining procedures were controlled by using an internal standard. The ion exchange chromatography made the greatest contribution to experimental error, imposing a minimum loading requirement of 0.1 mumol of each acid for adequate precision. Organic acid profiles were determined for seven wheat cultivars (Triticum aestivum cv Carazinho, Teal, Lance, Warigal, Isis, Maringa, and BH1146) grown on gravel in solution culture for 30 days. Profiles were simple, consisting of only malic, aconitic, and citric acids, with levels of each acid for all varieties falling within the range 2-5 mumol/g fresh tissue. Storage of s les led to a large increase in s ling error and increased the amount of extractable citric acid.
Publisher: American Chemical Society (ACS)
Date: 08-01-2013
DOI: 10.1021/AC302925F
Abstract: Digital polymerase chain reaction (dPCR) is potentially a primary method for quantifying target DNA regions in a background of nontarget material and is independent of external calibrators. Accurate dPCR measurements require single-molecule detection by conventional PCR assays that may be subject to bias due to inhibition, interference, or sequence-derived PCR inefficiency. Elimination or control of such biases is essential for validation of PCR assays, but this may require a substantial investment in resources. Here we present a mechanism for DNA quantification that does not require PCR assay validation in situations where target DNA quantity is high enough to be measured by physical techniques such as quantitative high-performance liquid chromatography (HPLC) or electrophoresis. A commercially available DNA marker derived from pUC19 was quantified by dPCR and was then used to calibrate an HPLC measuring system for quantifying a DNA licon that had a high content of guanidine and cytidine. The dPCR-calibrated HPLC measurement was verified by independent measurement using isotope dilution mass spectrometry (IDMS). HPLC quantification, calibrated with dPCR or IDMS measured DNA markers, provides an effective method for certifying the quantity of genetic reference materials that may be difficult to analyze by PCR. These secondary reference materials may then be used to validate and calibrate quantitative PCR measurements and thus could expand the breadth of applications for which traceability to the International System of Units is possible.
Publisher: American Chemical Society (ACS)
Date: 16-06-2009
DOI: 10.1021/AC900806Y
Abstract: In response to the sovereign requirement for national standards the National Measurement Institute, Australia (NMIA) has developed a measuring system using isotope dilution mass spectrometry (IDMS) to certify forensic aqueous ethanol solutions. NMIA participated in an international study, CCQM-K27, organized under the auspices of the International Committee for Weights and Measures to compare our measuring system with the techniques being used for certifying aqueous ethanol solutions in other metrology institutes. This comparison provided objective evidence that the measuring system developed was fit for the purpose of certifying aqueous ethanol solutions that ranged in concentration from 0.8 mg/g to 120 mg/g. A complete measurement uncertainty budget is presented and shows that the largest contribution to measurement uncertainty was from method precision followed by the contribution from the calibration solution. The fundamental technology of the measuring system was gas chromatography of the aqueous ethanol solutions using porous layer open tubular columns, and this effectively produced peak area measurements with both GC/MS and GC-FID. It was found that deactivation of the chromatographic system was critical for obtaining reproducible peak shapes and peak area measurements. A range of measuring systems, all using this gas chromatographic technology, was investigated. When conditions were carefully controlled there was no difference in measurement results from GC-IDMS, GC/MS or GC-FID. There was also no difference in results from on-column or split injection systems. A significant issue with the IDMS system was the fragmentation of 13C2-ethanol to produce an ion with the same mass as the molecular ion of ethanol which lead to isobaric interference careful measurement of this fragmentation ratio was necessary to calculate accurate mass fraction values. NMIA has adopted the GC-IDMS split measuring system to certify aqueous ethanol solutions for Australian legal requirements since this measuring system provided higher analytical specificity than GC-FID, accuracy that was fit for purpose and was operationally less stringent than on-column techniques.
Publisher: American Chemical Society (ACS)
Date: 03-06-2008
DOI: 10.1021/AC800270U
Abstract: Highly accurate measurements of the amount of substance of organic molecules in a test material can be obtained using exactly matched calibration solutions and internal standards that are labeled with stable isotope atoms by measuring the amount ratio of analyte to internal standard using mass spectrometry. Estimating the uncertainty of quantitative measurements of organic molecules is a means of evaluating accuracy and of establishing traceability to the International System of Units (SI) and requires a measurement function that fully describes the measuring system. This paper presents the derivation of the equation (measurement function) that describes this complete measurement after the internal standard has equilibrated with the test material matrix. It is similar to the equation for inorganic measurements using isotope dilution techniques, but potential biases during chemical processing arising from whole organic molecule analysis compared to inorganic atomic analysis required greater investigation of the yield factors that occur during organic molecule measurements. In the new equation, a series of ratios of proportionality factors are used to relate the amount of substance in a test material to chromatographic peak area ratios corresponding to mass spectrometer ion current ratios. All the proportionality factors are grouped together to define a measuring system factor F(X), the value of which is determined by the fundamental chemical processes affecting the yields of analyte, internal standard, and reference standard of the analyte in the measurement process. Any factors in the measurement process that affect the mole ratio of analyte to internal standard in the calibration solution differently from the test solution will result in a nonunity value for F(X) and a proportional bias to the measurement, and in this way F(X) represents the concept of recovery of the amount ratio of analyte to internal standard. Thus highly accurate measurements require F(X) or its constituent factors to be evaluated. In addition, the uncertainty in the evaluation of F(X) or of its constituent factors must be included in a complete uncertainty estimation of the analytical procedure. The many different permutations of proportionality factor ratios that may result in a unity value of F(X) are discussed resulting in a case for evaluating F(X) rather than the more common practice of evaluating in idual factors for each major stage of the measurement procedure. Since the new measurement function describes the complete chemical process that constitutes the measurement, traceability to the SI is assured when all factors in the function are measured traceably and have their associated uncertainty estimated correctly. Ignoring F(X) would invalidate traceability to the SI and would prevent a complete estimation of measurement uncertainty.
Publisher: American Chemical Society (ACS)
Date: 30-11-2016
DOI: 10.1021/ACS.ANALCHEM.6B03076
Abstract: Enumeration-based determination of DNA copy-concentration was assessed through an international comparison among national metrology institutes (NMIs) and designated institutes (DIs). Enumeration-based quantification does not require a calibration standard thereby providing a route to "absolute quantification", which offers the potential for reliable value assignments of DNA reference materials, and International System of Units (SI) traceability to copy number 1 through accurate counting. In this study, 2 enumeration-based methods, flow cytometric (FCM) counting and the digital polymerase chain reaction (dPCR), were compared to quantify a solution of the pBR322 plasmid at a concentration of several thousand copies per microliter. In addition, 2 orthogonal chemical-analysis methods based on nucleotide quantification, isotope-dilution mass spectrometry (IDMS) and capillary electrophoresis (CE) were applied to quantify a more concentrated solution of the plasmid. Although 9 dPCR results from 8 laboratories showed some dispersion (relative standard deviation [RSD] = 11.8%), their means were closely aligned with those of the FCM-based counting method and the orthogonal chemical-analysis methods, corrected for gravimetric dilution factors. Using the means of dPCR results, the RSD of all 4 methods was 1.8%, which strongly supported the validity of the recent enumeration approaches. Despite a good overall agreement, the in idual dPCR results were not sufficiently covered by the reported measurement uncertainties. These findings suggest that some laboratories may not have considered all factors contributing to the measurement uncertainty of dPCR, and further investigation of this possibility is warranted.
Publisher: Springer Science and Business Media LLC
Date: 12-06-2007
Publisher: Springer Science and Business Media LLC
Date: 20-06-2014
DOI: 10.1007/S00216-014-7914-5
Abstract: Hypermethylation at promoter regions of tumour suppressor genes is diagnostic for many cancers. Many genomic regions that may be the targets for clinical diagnostic assays have been identified through use of measuring systems reliant on bisulphite conversion, but few of these promising markers are in clinical use. The comparability of a widely used DNA methylation measuring system involving bisulphite conversion was evaluated by supplying three experienced centres with methylated DNA reference material mixtures that were independently prepared and characterised by mass spectrometry and high-pressure liquid chromatography. A replication scheme was designed to evaluate reproducibility of key analytical steps within and between laboratories by regression analysis. In general, methylation was underestimated and methylation ratio values were highly variable. The difference in methylation ratio between CpG sites was the key contributor to variable results. The CpG site effect followed a similar pattern at all centres and at all methylation levels examined indicating that sequence context had a major effect on methylation ratio measurement using the bisulphite conversion process. The magnitude of underestimation combined with the variability of measurements between CpG sites compromises the concept of measuring genomic regional methylation by averaging the methylation ratios of many CpG sites. There were no significant differences in replicate bisulphite conversions or s le work-up and instrument analysis at each centre thus making this technique suitable for comparative intralaboratory investigations. However, it may not be suitable for a routine diagnostic assay without extensive standardisation efforts.
Publisher: American Chemical Society (ACS)
Date: 05-1983
DOI: 10.1021/AC00257A004
Publisher: Cold Spring Harbor Laboratory
Date: 06-09-2023
Publisher: Elsevier BV
Date: 1988
Publisher: Elsevier BV
Date: 1987
Publisher: Elsevier BV
Date: 08-1982
No related grants have been discovered for Daniel Burke.