Biomedical subjects

David L Duewer

Publications and source records attributed to David L Duewer.

13 recordsLinked to original sources

PubMed2006

Multiplex_QA: an exploratory quality assessment tool for multiplexed electrophoretic assays.

Multiplex_QA is a data analysis tool for visualizing short- and long-term changes in the performance of multiplexed electrophoretic assays, particularly the commercial short tandem repeat (STR) kits used by the human forensic identity community. A number of quality metrics are calculated from the signal collected for the internal size standard included in nearly all multiplex assays. These quality metrics are related to the signal intensity, symmetry, retention, resolution, and noise of data collected by capillary electrophoresis systems. Interlocking graphical displays enable the identification of changes in the quality metrics with time, evaluation of relationships among the metrics, and detailed examination of electropherographic features of particularly interesting analyses. While primarily intended for exploring which metrics are most useful for documenting data quality, the current version of the tool is sufficiently robust for use by forensic scientists with an interest in data analysis and access to a fast desktop computer.

DNA↗

PubMed2005

Locus-specific brackets for reliable typing of Y-chromosome short tandem repeat markers.

Short tandem repeat (STR) loci, widely used as genetic markers in disease diagnostic studies and human identity applications, are traditionally genotyped through comparison of allele sizes to a sequenced allelic ladder. Allelic ladders permit a floating bin allele calling method to be utilized, which enables reliable allele calling across laboratories, instrument platforms, and electrophoretic conditions. Precise sizing methods for STR allele calling involving fixed bins can also be used when a high degree of precision has been demonstrated within an instrument platform and a set of electrophoretic conditions. An alternative method for reliable genotyping of STR markers, locus-specific brackets (LSBs), is introduced here. LSBs are artificial alleles created through molecular biology manipulations to be shorter or longer than alleles commonly seen in populations under investigation. The size and repeat number of measured alleles are interpolated between the two LSB products that are mixed with the polymerase chain reaction-amplified STR alleles. The advantages and limitations of the LSB approach are described along with a concordance study between the LSB typing approach and other STR typing methods. Complete agreement was observed with 162 samples studied at 5 Y-chromosome loci.

Alleles↗

PubMed2005

Standard reference material 2036 near-infrared reflection wavelength standard.

Standard Reference Material 2036 (SRM 2036) is a certified transfer standard intended for the verification and calibration of the wavelength/wavenumber scale of near-infrared (NIR) spectrometers operating in diffuse or trans-reflectance mode. SRM 2036 Near-Infrared Wavelength/Wavenumber Reflection Standard is a combination of a rare earth oxide glass of a composition similar to that of SRM 2035 Near-Infrared Transmission Wavelength/Wavenumber Standard and SRM 2065 Ultraviolet-Visible-Near-Infrared Transmission Wavelength/Wavenumber Standard, but is in physical contact with a piece of sintered poly(tetrafluoroethylene) (PTFE). The combination of glass contacted with a nearly ideal diffusely reflecting backing provides reflection-absorption bands that range from 15% R to 40% R. SRM 2036 is certified for the 10% band fraction air wavelength centroid location, (10%)B, of seven bands spanning the spectral region from 975 nm to 1946 nm. It is also certified for the vacuum wavenumber (10%)B of the same seven bands in the spectral region from 10 300 cm(-1) to 5130 cm(-1) at 8 cm(-1) resolution. Informational values are provided for the locations of thirteen additional bands from 334 nm to 804 nm.

Fiber Optic Technology↗

PubMed2005

Mitochondrial DNA typing screens with control region and coding region SNPs.

Mitochondrial DNA (mtDNA) analysis has found an important niche in forensic DNA typing. It is used with highly degraded samples or low-copy number materials such as might be found from shed hair or bones exposed to severe environmental conditions. The primary advantage of mtDNA is that it is present in high copy number within cells and therefore more likely to be recovered from highly degraded specimens. A major disadvantage to traditional forensic mtDNA analysis is that it is time-consuming and labor-intensive to generate and review the 610 nucleotides of sequence information commonly targeted in hypervariable regions I and II (HVI and HVII) of the control region. In addition, common haplotypes exist in HVI/HVII mtDNA sequences that can reduce the ability to differentiate two unrelated samples. In this report we describe the utility of two newly available screening assays for rapid exclusion of non-matching samples. The LINEAR ARRAY mtDNA HVI/HVII Region-Sequencing Typing Kit (Roche Applied Science, Indianapolis, IN) was used to type 666 individuals from U.S. Caucasian, African American, and Hispanic groups. Processing of the LINEAR ARRAY probe panels "mito strips" was automated on a ProfiBlot workstation. Observable variation in 666 individuals is reported and frequencies of the mitotypes within and between populations are presented. Samples exhibiting the most common Caucasian mitotype were subdivided with a multiplexed amplification and detection assay using eleven single nucleotide polymorphisms in the mitochondrial genome. These types of screening assays should enable more rapid evaluation of forensic casework samples such that only samples not excluded would be subjected to further characterization through full HVI/HVII mtDNA sequence analysis.

Automation↗

PubMed2005

Results from the NIST 2004 DNA Quantitation Study.

For optimal DNA short tandem repeat (STR) typing results, the DNA concentration ([DNA]) of the sample must be accurately determined prior to the polymerase chain reaction (PCR) amplification step in the typing process. In early 2004, the National Institute of Standards and Technology (NIST) conducted an interlaboratory study to help assess the accuracy of DNA quantitation in forensic DNA laboratories. This study was designed with four primary purposes: (1) to examine concentration effects and to probe performance at the lower DNA concentration levels that are frequently seen in forensic casework; (2) to examine consistency with various methodologies across multiple laboratories; (3) to examine single versus multiple source samples; and (4) to study DNA stability over time and through shipping in two types of storage tubes. Eight DNA samples of [DNA] from 0.05 ng/microL to 1.5 ng/microL were distributed. A total of 287 independent data sets were returned from 80 participants. Results were reported for 19 different DNA quantitation methodologies. Approximately 65% of the data were obtained using traditional slot blot hybridization methods; 21% were obtained using newly available quantitative real-time PCR (Q-PCR) techniques. Information from this interlaboratory study is guiding development of a future NIST Standard Reference Material for Human DNA Quantitation, SRM 2372.

DNA↗

PubMed2004

NIST mixed stain study 3: signal intensity balance in commercial short tandem repeat multiplexes.

Short-tandem repeat (STR) allelic intensities were collected from more than 60 forensic laboratories for a suite of seven samples as part of the National Institute of Standards and Technology-coordinated 2001 Mixed Stain Study 3 (MSS3). These interlaboratory challenge data illuminate the relative importance of intrinsic and user-determined factors affecting the locus-to-locus balance of signal intensities for currently used STR multiplexes. To varying degrees, seven of the eight commercially produced multiplexes used by MSS3 participants displayed very similar patterns of intensity differences among the different loci probed by the multiplexes for all samples, in the hands of multiple analysts, with a variety of supplies and instruments. These systematic differences reflect intrinsic properties of the individual multiplexes, not user-controllable measurement practices. To the extent that quality systems specify minimum and maximum absolute intensities for data acceptability and data interpretation schema require among-locus balance, these intrinsic intensity differences may decrease the utility of multiplex results and surely increase the cost of analysis.

Alleles↗

PubMed2003

NIST Mixed Stain Study 3: DNA quantitation accuracy and its influence on short tandem repeat multiplex signal intensity.

The Mixed Stain Study 3 (MSS3) interlaboratory challenge exercise evaluated the 2001 performance of STR multiplex DNA typing systems using a set of seven DNA extracts of designed concentration and composition. This initial report focuses on the linkages connecting the measurement of the concentration of DNA ([DNA]) to the observed STR multiplex signal intensities. There is a causal relationship between [DNA] measurement accuracy and the efficiency of STR multiplex analysis. There are no intrinsic measurement performance differences among the [DNA] measurement technologies reported. However, there are large differences in the efficiencies of amplification, separation, and detection among participants using the same nominal measurement systems.

DNA↗

PubMed2003

Rare-earth glass reference materials for near-infrared spectrometry: correcting and exploiting temperature dependencies.

Quantitative descriptions of the location of seven near-infrared absorption bands as functions of temperature 5-50 degrees C are presented here for three recently introduced wavelength/wavenumber Standard Reference Materials (SRMs): SRM 2035, SRM 2065, and SRM 2036. For all bands in all three SRMs, locations are well described as linear models parametrized with the location at 0 degrees C (intercept) and the rate of location change per degrees C (slope). Since these materials were produced from compositionally similar melts, the slopes for each band are identical within measurement imprecision in all three SRMs; only minor differences are observed in the intercepts. Because the direction of change in location differs among the bands, it is possible to use the measured band locations to reliably estimate sample temperature. Two approaches to estimating temperature are evaluated: slope and measurement uncertainty-weighted means. While both methods work well with measurements made under well-characterized and stable environmental conditions, the more complex uncertainty-weighted analysis becomes relatively more predictive as the total measurement uncertainties increase.

Journal Article↗

PubMed2003

Certification of standard reference material 970, ascorbic acid in serum, and analysis of associated interlaboratory bias in the measurement process.

BACKGROUND: The accurate and reproducible measurement of ascorbic acid is essential in delineating the role of ascorbic acid as a diagnostic tool for human disease and for the comparison of data acquired by different laboratories. A stabilized pair of standards of ascorbic acid in human serum, which is compatible with most analytical methods, have been prepared. METHODS: The certification was based on the gravimetric addition of ascorbic acid to metaphosphoric acid-stabilized, ascorbic acid-depleted serum and NIST liquid chromatography-electrochemical measurements. The NIST results were analyzed statistically for homogeneity, and the expanded uncertainty of each SRM was calculated using all of the NIST data. An interlaboratory comparison exercise was also performed. RESULTS: These materials, Standard Reference Material (SRM) 970 Ascorbic Acid in Serum, Level I and Level II, are homogeneous and are certified to contain (10.07 +/- 0.21) and (30.57 +/- 0.28) mmol ascorbic acid/L of solution (expanded uncertainty), respectively. In the interlaboratory comparison (n = 17), the relative SDs for the two materials were 22% and 19%. CONCLUSIONS: Two lots of serum, each containing different amounts of ascorbic acid stabilized in metaphosphoric acid, have been prepared and characterized. Many laboratories provide inaccurate results.

Ascorbic Acid↗

PubMed2002

An international evaluation of holmium oxide solution reference materials for wavelength calibration in molecular absorption spectrophotometry.

Commercial spectrophotometers typically use absorption-based wavelength calibration reference materials to provide wavelength accuracy for their applications. Low-mass fractions of holmium oxide (Ho2O3) in dilute acidic aqueous solution and in glass matrixes have been favored for use as wavelength calibration materials on the basis of spectral coverage and absorption band shape. Both aqueous and glass Ho2O3 reference materials are available commercially and through various National Metrology Institutes (NMIs). Three NMIs of the North American Cooperation in Metrology (NORAMET) have evaluated the performance of Ho3-(aq)-based Certified Reference Materials (CRMs) under "routine" operating conditions using commercial instrumentation. The study was not intended to intercompare national wavelength scales but to demonstrate comparability of wavelength measurements among the participants and between two versions of the CRMs. It was also designed to acquire data from a variety of spectrophotometers for use in a NIST study of wavelength assignment algorithms and to provide a basis for a possible reassessment of NIST-certified Ho3+(aq) band locations. The resulting data show a substantial level of agreement among laboratories, instruments, CRM preparations, and peak-location algorithms. At the same time, it is demonstrated that the wavelength comparability of the five participating instruments can actually be improved by calibrating all of the instruments to the consensus Ho3+(aq) band locations. This finding supports the value of absorption-based wavelength standards for calibrating absorption spectrophotometers. Coupled with the demonstrated robustness of the band position values with respect to preparation and measurement conditions, it also supports the concept of extending the present approach to additional NMIs in order to certify properly prepared dilute acidic Ho2O3 solution as an intrinsic wavelength standard.

Journal Article↗

PubMed2002

Polymerase chain reaction amplification of DNA from aged blood stains: quantitative evaluation of the "suitability for purpose" of four filter papers as archival media.

In collaboration with the Armed Forces Institute of Pathology's Department of Defense DNA Registry, the National Institute of Standards and Technology recently evaluated the performance of a short tandem repeat multiplex with dried whole blood stains on four different commercially available identification card matrixes. DNA from 70 stains that had been stored for 19 months at ambient temperature was extracted or directly amplified and then processed using routine methods. All four storage media provided fully typeable (qualitatively identical) samples. After standardization, the average among-locus fluorescence intensity (electropherographic peak height or area) provided a suitable metric for quantitative analysis of the relative amounts of amplifiable DNA in an archived sample. The amounts of DNA in Chelex extracts from stains on two untreated high-purity cotton linter pulp papers and a paper treated with a DNA-binding coating were essentially identical. Average intensities for the aqueous extracts from a paper treated with a DNA-releasing coating were somewhat lower but also somewhat less variable than for the Chelex extracts. Average intensities of directly amplified punches of the DNA-binding paper were much larger but somewhat more variable than the Chelex extracts. Approximately 25% of the observed variation among the intensity measurements is shared among the four media and thus can be attributed to intrinsic variation in white blood count among the donors. All of the evaluated media adequately "bank" forensically useful DNA in well-dried whole blood stains for at least 19 months at ambient temperature.

Blood Stains↗

PubMed2002

Associating gunpowder and residues from commercial ammunition using compositional analysis.

Qualitatively identifying and quantitatively determining the additives in smokeless gunpowder to calculate a numerical propellant to stabilizer (P/S) ratio is a new approach to associate handgun-fired organic gunshot residues (OGSR) with unfired powder. In past work, the P/S values of handgun OGSR and cartridges loaded with known gunpowders were evaluated. In this study, gunpowder and residue samples were obtained from seven boxes of commercial 38 caliber ammunition with the goals of associating cartridges within a box and matching residues to unfired powders, based on the P/S value and the qualitative identity of the additives. Gunpowder samples from four of the seven boxes of ammunition could be easily differentiated. When visual comparisons of the cartridge powders were considered in addition to composition, powder samples from all seven boxes of ammunition could be reliably differentiated. Handgun OGSR was also collected and evaluated in bulk as well as for individual particles. In some cases, residues could be reliably differentiated based on P/S and additive identity. It was instructive to evaluate the composition of individual unfired gunpowder and OGSR particles. We determined that both the numerical centroid and dispersity of the P/S measurements provide information for associations and exclusions. Associating measurements from residue particles with those of residue samples collected from a test firing of the same weapon and ammunition appears to be a useful approach to account for any changes in composition that occur during the firing process.

Calibration↗

PubMed2002

A quantitative comparison of smokeless measurements.

Measurements of the type and concentration of propellant and stabilizer additives in smokeless gunpowder are used by forensic scientists investigating the source of explosives and by military laboratories assuring the safety and efficacy of munitions. The National Institute of Standards and Technology recently assessed the state-of-the-practice of smokeless powder measurements through an international measurement comparison exercise. We here present results provided by the five participants (of 20 total) reporting quantitative as well as qualitative values for two handgun reloading powders. All five of these participants reported values for nitroglycerin (NG), ethyl centralite (EC), diphenylamine (DPA), and N-nitrosodiphenylamine (NnDPA). Several participants additionally reported the concentrations of secondary stabilizer decomposition products. The unstable NG propellant additive appears to be more susceptible to method-specific calibration biases then are the stabilizer additives. All results from one participant were strongly biased relative to those of the other four. The within-participant measurement uncertainties for all analytes were self-reported to be 1 to 5% relative; among the four concordant participants, the measurement ranges are 5 to 10% relative. There was little consistency among the participants as to what components of measurement variance were included in their uncertainty statements. A discussion of the certainties in these measurements and factors that affect the accuracy of gunpowder additive determinations is presented.

Journal Article↗