Performance of a method for weighting a range in the number of contributors in probabilistic genotyping.

Uncertainty in the assignment of the number of contributors (NoC) can be encountered, particularly in higher-order mixtures, where alleles may be shared between contributors, may have dropped out, or may be masked by the stutter artefacts or allelic peaks of a more dominant contributor. Most probabilistic genotyping software requires the assignment of NoC prior to interpretation. NoC has been described as a nuisance parameter. Taylor et al. [1] describe a method to weigh the probability of the profile under different values of N and incorporate this into a likelihood ratio (LR). Within this paper we explore the performance of this variable number of contributors (varNoC) method programmed within the probabilistic genotyping software STRmix™. The desired combination of performance and runtime was obtained using the default STRmix™ version 2.7 MCMC settings in conjunction with a 2.5 % hyper-rectangle range, at least 10,000 naïve MC iterations and 8 MCMC chains. The varNoC LR demonstrated the typical sensitivity and specificity behaviour seen in previous studies, with a high level of reproducibility given repeat analyses. Profiles previously demonstrating ambiguity in the NoC assigned using conventional estimation methods, were able to be reliably interpreted and a varNoC LR assigned.

STRmix™ collaborative exercise on DNA mixture interpretation.

An intra and inter-laboratory study using the probabilistic genotyping (PG) software STRmix™ is reported. Two complex mixtures from the PROVEDIt set, analysed on an Applied Biosystems™ 3500 Series Genetic Analyzer, were selected. 174 participants responded. For Sample 1 (low template, in the order of 200 rfu for major contributors) five participants described the comparison as inconclusive with respect to the POI or excluded him. Where LRs were assigned, the point estimates ranging from 2 × 104 to 8 × 106. For Sample 2 (in the order of 2000 rfu for major contributors), LRs ranged from 2 × 1028 to 2 × 1029. Where LRs were calculated, the differences between participants can be attributed to (from largest to smallest impact): This study demonstrates a high level of repeatability and reproducibility among the participants. For those results that differed from the mode, the differences in LR were almost always minor or conservative.

Internal validation of STRmix™ - A multi laboratory response to PCAST.

We report a large compilation of the internal validations of the probabilistic genotyping software STRmix™. Thirty one laboratories contributed data resulting in 2825 mixtures comprising three to six donors and a wide range of multiplex, equipment, mixture proportions and templates. Previously reported trends in the LR were confirmed including less discriminatory LRs occurring both for donors and non-donors at low template (for the donor in question) and at high contributor number. We were unable to isolate an effect of allelic sharing. Any apparent effect appears to be largely confounded with increased contributor number.

Allele frequency database for GlobalFiler™ STR loci in Australian and New Zealand populations.

We assign autosomal allele proportions for Caucasian, Asian, self-declared Aboriginal and pure Aboriginal populations from Australia and Caucasian and Eastern and Western Polynesian populations from New Zealand. Population sample sizes vary from 122 to 528. All populations underwent tests for the presence of allelic dependencies (i.e. departures from the expectations of Hardy Weinberg and Linkage equilibrium) and some large dependencies were observed in the Australian Aboriginal populations. We provide allele frequency files for all populations examined.

Does nitrous oxide labor analgesia influence the pattern of neuraxial analgesia usage? An impact study at an academic medical center.

STUDY OBJECTIVE: To compare the rate of epidural use before and after the implementation of nitrous oxide (N2O). DESIGN: Data were obtained from a nursing database of N2O usage and our obstetric anesthesia database. We compared 8 months before and 8 months after the introduction of N2O. It was available 24 h/d, 7 d/wk, consistent with neuraxial analgesia availability. Epidural utilization before and after introduction of N2O was compared using χ2 analysis. SETTING: Labor and delivery floor. MAIN RESULTS: Total number of births over the study period was 8539: 4315 pre-N2O and 4224 post-N2O. The rate of epidural usage was 77% pre-N2O and 74% after N2O (P= not significant, χ2). A total of 762 patients used N2O. Monthly analysis showed no change in pattern of neuraxial analgesia use in post-N2O period compared with the pre-N2O period. CONCLUSION: The introduction of N2O for labor analgesia was not associated with any change in our rate of labor epidural utilization. Under the conditions of our study, these results suggest that N2O does not discourage neuraxial use for labor pain relief.

Developmental validation of STRmix™, expert software for the interpretation of forensic DNA profiles.

In 2015 the Scientific Working Group on DNA Analysis Methods published the SWGDAM Guidelines for the Validation of Probabilistic Genotyping Systems [1]. STRmix™ is probabilistic genotyping software that employs a continuous model of DNA profile interpretation. This paper describes the developmental validation activities of STRmix™ following the SWGDAM guidelines. It addresses the underlying scientific principles, and the performance of the models with respect to sensitivity, specificity and precision and results of interpretation of casework type samples. This work demonstrates that STRmix™ is suitable for its intended use for the interpretation of single source and mixed DNA profiles.

Investigating a common approach to DNA profile interpretation using probabilistic software.

Recently there has been a drive for standardisation of DNA profile interpretation within and between different forensic laboratories. The continuous interpretation software STRmix™ has been adopted for use by laboratories in Australia and New Zealand for profile interpretation. Within this paper we examine the concordance in profile interpretation of three crime samples by twenty different analysts across twelve different international laboratories using STRmix™. The three profiles selected for this study exhibited a range of template and complexity. The use of probabilistic software has compelled a level of concordance between different analysts however there remain differences within profile interpretation, particularly with the objective assignment of the number of contributors to profiles.

An evaluation of potential allelic association between the STRs vWA and D12S391: implications in criminal casework and applications to short pedigrees.

An evaluation was carried out to determine the effect on routine forensic calculations when incorporating STRs D12S391 and vWA. These loci are co-located on the same arm of chromosome 12. It has been suggested that allelic association could result in over-estimates of strength-of-evidence calculations. In the first place, we argue that is very unlikely that genotypes collected from typical cosmopolitan forensic databases can provide meaningful information about effects attributable to physical linkage. Since admixture is the most likely cause of allelic association in modern populations we specifically evaluate this effect. We use computer simulation as the preferred approach to generate populations with disequilibrium and observe the effect on match probability. Although we have specifically evaluated the linkage between D12S391 and vWA, the methods described in this paper can be extended and generalized to evaluate linkage effects between any pair of loci where the recombination rate is known. Many jurisdictions apply a subpopulation correction following the standard method of Balding and Nichols. Such corrections would appear to be more than adequate to compensate for any increase in match probability that we were able to create by this admixture. Linkage is likely to have an appreciable effect on relatedness calculations in short pedigrees in some but not all instances. We examined those circumstances where an effect is likely and give formulae for some common situations. The complexity of these calculations is a cause for concern in some laboratories. We discuss possible strategies that might be employed and plausible effects.

The results of an experimental indoor hydroponic Cannabis growing study, using the 'Screen of Green' (ScrOG) method-Yield, tetrahydrocannabinol (THC) and DNA analysis.

The results of an indoor hydroponic Cannabis growth study are presented. It is intended that this work will be of assistance to those with an interest in determining an estimation of yield and value of Cannabis crops. Three cycles of six plants were grown over a period of 1 year in order to ascertain the potential yield of female flowering head material from such an operation. The cultivation methods used were selected to replicate typical indoor hydroponic Cannabis growing operations, such as are commonly encountered by the New Zealand Police. The plants were also tested to ascertain the percentage of the psychoactive chemical Δ-9 tetrahydrocannabinol (THC) present in the flowering head material, and were genetically profiled by STR analysis. Phenotypic observations are related to the data collected. The inexperience of the growers was evidenced by different problems encountered in each of the three cycles, each of which would be expected to negatively impact the yield and THC data obtained. These data are therefore considered to be conservative. The most successful cycle yielded an average of 881g (31.1oz) of dry, groomed female flowering head per plant, and over the whole study the 18 plants yielded a total of 12,360g (436.0oz), or an average of 687g (24.2oz) of dry head per plant. THC data shows significant intra-plant variation and also demonstrates inter-varietal variation. THC values for individual plants ranged from 4.3 to 25.2%. The findings of this study and a separate ESR research project illustrate that the potency of Cannabis grown in New Zealand has dramatically increased in recent years. DNA analysis distinguished distinct groups in general agreement with the phenotypic variation observed. One plant however, exhibiting a unique triallelic pattern at two of the five loci tested, while remaining phenotypically indistinguishable from three other plants within the same grow.

Allele frequencies for the four major sub-populations of New Zealand for the 15 Identifiler loci.

Allele frequencies for the 15 STRs included in the AmpFlSTR Identifiler (Applied Biosystems Incorporated, Foster City, CA, USA) STR DNA profiling system have been determined for the four major sub-populations of New Zealand. The data set is comprised of DNA profiles obtained over a 12-year period and includes profiles obtained using the Second Generation Multiplex (SGM, Forensic Science Services, UK), and the AmpFlSTR SGMPlus (Applied Biosystems Incorporated, Foster City, CA, USA) STR DNA profiling systems.