Perspectives of people experiencing homelessness with recent non-fatal street drug overdose on the Pharmacist and Homeless Outreach Engagement and Non-medical Independent prescribing Rx (PHOENIx) intervention.

INTRODUCTION: In Scotland, a third of all deaths of people experiencing homelessness (PExH) are street-drug-related, and less than half of their multiple physical- and mental health conditions are treated. New, holistic interventions are required to address these health inequalities. PHOENIx (Pharmacist Homeless Outreach Engagement and Non-medical Independent prescribing Rx) is delivered on outreach by National Health Service (NHS) pharmacist independent prescribers in partnership with third sector homelessness charity workers. We describe participant's perspectives of PHOENIx. METHODS: This study aims to understand experiences of the PHOENIx intervention by participants recruited into the active arm of a pilot randomised controlled trial (RCT). Semi-structured in-person interviews explored participants' evaluation of the intervention. In this study, the four components (coherence, cognitive participation, collective action, reflexive monitoring) of the Normalisation Process Theory (NPT) framework underpinned data collection and analyses. RESULTS: We identified four themes that were interpreted within the NPT framework that describe participant evaluation of the PHOENIx intervention: differentiating the intervention from usual care (coherence), embedding connection and consistency in practice (cognitive participation), implementation of practical and emotional operational work (collective action), and lack of power and a commitment to long-term support (reflexive monitoring). Participants successfully engaged with the intervention. Facilitators for participant motivation included the relationship-based work created by the PHOENIx team. This included operational work to fulfil both the practical and emotional needs of participants. Barriers included concern regarding power imbalances within the sector, a lack of long-term support and the impact of the intervention concluding. CONCLUSIONS: Findings identify and describe participants' evaluations of the PHOENIx intervention. NPT is a theoretical framework facilitating understanding of experiences, highlighting both facilitators and barriers to sustained engagement and investment. Our findings inform future developments regarding a subsequent definitive RCT of PHOENIx, despite challenges brought about by challenging micro and macro-economic and political landscapes.

Using Patient Preferences in Health Technology Assessment: Evaluating Quality-Adjusted Survival Equivalents (QASE) for the Quantification of Non-health Benefits.

Interest in using patient preference (PP) data alongside traditional economic models in health technology assessment (HTA) is growing, including using PP data to quantify non-health benefits. However, this is limited by a lack of standardised methods. In this article, we describe a method for using discrete choice experiment (DCE) data to estimate the value of non-health benefits in terms of quality-adjusted survival equivalence (QASE), which is consistent with the concept of value prevalent among HTA agencies. We describe how PP data can be used to estimate QASE, assess the ability to test the face-validity of QASE estimates of changes in mode of administration calculated from five published DCE oncology studies and review the methodological and normative considerations associated with using QASE to support HTA. We conclude that QASE may have some methodological advantages over alternative methods, but this requires DCEs to estimate second-order effects between length and quality of life. In addition, empirical work has yet to be undertaken to substantiate this advantage and demonstrate the validity of QASE. Further work is also required to align QASE with normative objectives of HTA agencies. Estimating QASE would also have implications for the conduct of DCEs, including standardising and defining more clear attribute definitions.

Wave propagation in the marginal ice zone: connections and feedback mechanisms within the air-ice-ocean system.

The propagation of ocean surface waves within the marginal ice zone (MIZ) is a defining phenomenon of this dynamic zone. Over decades of study, a variety of methods have been developed to observe and model wave propagation in the MIZ, with a common focus of determining the attenuation of waves with increasing distance into the MIZ. More recently, studies have begun to explore the consequences of wave attenuation and the coupled processes in the air-ice-ocean-land system. Understanding these coupled processes and effects is essential for accurate high-latitude forecasts. As waves attenuate, their momentum and energy are transferred to the sea ice and upper ocean. This may compact or expand the MIZ, depending on the conditions, while simultaneously modulating the wind work on the system. Wave attenuation is also a key process in coastal dynamics, where land-fast ice has historically protected both natural coasts and coastal infrastructure. With observed trends of increasing wave activity and retreating seasonal ice coverage, the propagation of waves within the MIZ is increasingly important to regional and global climate trends. This article is part of the theme issue 'Theory, modelling and observations of marginal ice zone dynamics: multidisciplinary perspectives and outlooks'.

Examining patient and professional perspectives in the UK for gene therapy in haemophilia.

INTRODUCTION: With the development of gene therapy for people with haemophilia (PWH), it is important to understand how people impacted by haemophilia (PIH) and clinicians prioritise haemophilia treatment attributes to support informed treatment decisions. OBJECTIVE: To examine the treatment attribute preferences of PIH and clinical experts in the United Kingdom (UK) and to develop a profile of gene therapy characteristics fit for use in future discrete choice experiments (DCEs). METHODS: Semi-structured interviews were conducted with PIH (n = 14) and clinical experts (n = 6) who ranked pre-defined treatment attributes by importance. Framework analysis was conducted to identify key themes and treatment attributes; points were allocated based on the rankings. Synthesis of results by a multidisciplinary group informed development of a profile of gene therapy characteristics for use in future research. RESULTS: Key themes identified by PIH and clinical experts included patient relevant features and the importance of 'informed decision making'. The six top-ranked treatment attributes were 'effect on factor level' (79 points), 'uncertainty regarding long-term risks' (57 points), 'impact on daily life' (41 points), 'frequency of monitoring' (33 points), 'impact on ability to participate in physical activity' (29 points), and 'uncertainty regarding long-term benefits' (28 points). The final treatment characteristics were categorised as therapeutic option, treatment effectiveness, safety concerns, impact on self-management and quality of life (role limitations). CONCLUSION: We identified several gene therapy characteristics important to PIH and clinicians in the UK. These characteristics will be used in a future DCE to further investigate patient preferences for gene therapy.

Interpretation and reporting of mixed DNA profiles by seven forensic laboratories in the UK and Ireland.

In 2014, the UK Forensic Science Regulator (FSR) commissioned a collaborative trial to assess the methods used by forensic service providers (FSPs) in the UK and Ireland for analysis, interpretation and reporting of mixed DNA profiles. Five different mixed samples of varying complexity with supporting mock case circumstances were tested using SGMPlus™ and the newly introduced DNA-17(+) multiplexes and reported by participating laboratories. The results demonstrated a high degree of consistency in analytical methods and allele designations, but some variation in the statistical evaluation and reporting of results. Some of the differences noted were attributable to the major technology change to 17(+)-STR systems which had recently been implemented across the UK at that time. The FSR made recommendations based on the trial outcomes which were intended to produce a more consistent approach to mixtures analysis, interpretation and reporting. Four years later, the Association of Forensic Science Providers (AFSP) repeated the trial, with all major UK and Ireland FSPs (both public sector and private companies) again participating. This second trial used the same mixture set as the 2014 trial but was focussed on the methods for interpretation and evaluation. Since 2014, all UK and Ireland FSPs have implemented probabilistic statistical software using continuous models enabling statistical evaluation of more complex mixtures than was possible in 2014. The trial was therefore aimed at investigating the value of these improved capabilities and also to investigate if there appeared to be marked differences between the different software tools in use in the UK. The results demonstrate a high degree of concordance within and between FSPs and across different evaluation models, and will provide important support for the use of such models in evaluation of mixed DNA profiles.

A warm jet in a cold ocean.

Unprecedented quantities of heat are entering the Pacific sector of the Arctic Ocean through Bering Strait, particularly during summer months. Though some heat is lost to the atmosphere during autumn cooling, a significant fraction of the incoming warm, salty water subducts (dives beneath) below a cooler fresher layer of near-surface water, subsequently extending hundreds of kilometers into the Beaufort Gyre. Upward turbulent mixing of these sub-surface pockets of heat is likely accelerating sea ice melt in the region. This Pacific-origin water brings both heat and unique biogeochemical properties, contributing to a changing Arctic ecosystem. However, our ability to understand or forecast the role of this incoming water mass has been hampered by lack of understanding of the physical processes controlling subduction and evolution of this this warm water. Crucially, the processes seen here occur at small horizontal scales not resolved by regional forecast models or climate simulations; new parameterizations must be developed that accurately represent the physics. Here we present novel high resolution observations showing the detailed process of subduction and initial evolution of warm Pacific-origin water in the southern Beaufort Gyre.

An investigation of two methods of DNA recovery from fired and unfired 9 mm ammunition.

Cartridge cases are often recovered from crime scenes involving firearms and, in the United Kingdom (where gun possession is strictly controlled), these are commonly from 9 mm calibre ammunition. The ability to obtain informative DNA profiles from touch DNA on recovered cartridges could have a significant impact on the investigation of that type of offence. However, this avenue may not be routinely considered as investigators in the UK have historically had a low expectation of obtaining useful DNA profiles. This stance may not be unreasonable given that (a) only trace amounts of DNA are likely to have been transferred onto the cartridge cases through handling; and (b) when the cartridge is spent, the potential deterioration of that DNA caused by the act of discharging the weapon. We introduce a novel semi-automatable method using direct lysis for the recovery of DNA from ammunition and compare it with a traditional double-swabbing method (using wet and dry swabs). DNA profiling of the DNA recovered using both methods was carried out using the ESI17 FAST STR system (Promega). This demonstrated a significant increase in DNA recovery using the direct lysis approach, and correspondingly improved STR results. We also investigated the effect on the recovery and profiling of DNA from fired, and unfired, 9 mm cartridges using the direct lysis technique. These results demonstrate that DNA suitable for STR analysis can still be recovered from fired ammunition with only slightly reduced yields compared to unfired ammunition. In these experiments, the handler of the ammunition was most commonly either the sole contributor or the major contributor to the recovered DNA profile.

A comprehensive study of allele drop-in over an extended period of time.

Some probabilistic mixture programmes take into account the presence of additional alleles by utilising drop-in models [1-4]. Although the precise details of the various models vary, at their core, they all rely on two basic assumptions - (1) that drop-in events occur independently of each other and (2) the frequency of individual dropped-in alleles mirrors the composition within some specified population. In order to examine the robustness of these assumptions, we have collected data on allele drop-in and contamination events in 28,842 negative control samples processed over a three year period in our DNA crime laboratory. These data were used to characterise drop-in events, and to identify trends in drop-in rates over time and between control types. In addition, we carried out an experiment using genomic DNA that had been highly diluted and demonstrate that, at these levels, drop-in events become indistinguishable from low level genomic contamination. Our results show that drop-in alleles are not necessarily independent random events. Moreover, a comparison between our data and UK frequency databases also suggests that the frequency of individual dropped-in alleles does not mirror the general population frequencies.

An empirical investigation into the effectiveness of genetic genealogy to identify individuals in the UK.

The use of genetic genealogy techniques to identify Joseph James DeAngelo as the prime suspect in the Golden State Killer case in 2018 has opened up a new approach to investigation of cold cases. Since that breakthrough, genetic genealogy methods have been reported to be applied to around 100 cases. To date, all of these reports relate to investigations in the US, where the high uptake of "direct-to-consumer" (DTC) genetic testing by individuals conducting private ancestral research has provided the necessary publicly available data for successful forensic investigations. We have conducted a study to assess the likely effectiveness of genetic genealogy techniques if applied to investigations in the UK. Ten volunteers provided their own SNP array data, downloaded from a DTC provider of their choice. These data sets were anonymised and uploaded to the GEDmatch Genesis genealogy website, mimicking data sets from unsourced crime samples or unidentified human remains. A team of experienced genealogists then attempted to identify the donors of the anonymised data sets by working with matches on the database and identifying points where the matches' trees intersect to determine their shared family lineages which were further investigated using traditional resources (such as birth, marriage, death and census records, social media and online family trees). Through these methods, four of the ten donors were identified, at least to the level of one of a set of siblings. This confirms that, despite the over-representation of US citizens on publicly accessible genealogy databases, there is still potential for effective use in investigations outside the US where legislation permits. One of our four identified individuals was of Indian heritage (via St Vincent and the Grenadines) highlighting that in the right circumstances individuals of non-European origin can be identified.

A Phase I Study of Pegylated Arginine Deiminase (Pegargiminase), Cisplatin, and Pemetrexed in Argininosuccinate Synthetase 1-Deficient Recurrent High-grade Glioma.

PURPOSE: Patients with recurrent high-grade gliomas (HGG) are usually managed with alkylating chemotherapy ± bevacizumab. However, prognosis remains very poor. Preclinically, we showed that HGGs are a target for arginine depletion with pegargiminase (ADI-PEG20) due to epimutations of argininosuccinate synthetase (ASS1) and/or argininosuccinate lyase (ASL). Moreover, ADI-PEG20 disrupts pyrimidine pools in ASS1-deficient HGGs, thereby impacting sensitivity to the antifolate, pemetrexed. PATIENTS AND METHODS: We expanded a phase I trial of ADI-PEG20 with pemetrexed and cisplatin (ADIPEMCIS) to patients with ASS1-deficient recurrent HGGs (NCT02029690). Patients were enrolled (01/16-06/17) to receive weekly ADI-PEG20 36 mg/m2 intramuscularly plus pemetrexed 500 mg/m2 and cisplatin 75 mg/m2 intravenously once every 3 weeks for up to 6 cycles. Patients with disease control were allowed ADI-PEG20 maintenance. The primary endpoints were safety, tolerability, and preliminary estimates of efficacy. RESULTS: Ten ASS1-deficient heavily pretreated patients were treated with ADIPEMCIS therapy. Treatment was well tolerated with the majority of adverse events being Common Terminology Criteria for Adverse Events v4.03 grade 1-2. The best overall response was stable disease in 8 patients (80%). Plasma arginine was suppressed significantly below baseline with a reciprocal increase in citrulline during the sampling period. The anti-ADI-PEG20 antibody titer rose during the first 4 weeks of treatment before reaching a plateau. Median progression-free survival (PFS) was 5.2 months (95% confidence interval (CI), 2.5-20.8) and overall survival was 6.3 months (95% CI, 1.8-9.7). CONCLUSIONS: In this recurrent HGG study, ADIPEMCIS was well tolerated and compares favorably to historical controls. Additional trials of ADI-PEG20 in HGG are planned.

Changes in Body Mass Index and Rates of Death and Transplant in Hemodialysis Patients: A Latent Class Joint Modeling Approach.

BACKGROUND: The relationship between body mass index (BMI) and patient survival in end-stage kidney disease is not well understood and has been the subject of much debate over recent years. METHODS: This study used a latent class joint modeling approach to identify latent groups that underpinned associations between patterns of change in BMI during hemodialysis and two competing events: transplant and death without transplant. We included all adult patients who initiated chronic hemodialysis treatment in Australia or New Zealand between 2005 and 2014. RESULTS: There were 16,414 patients included in the analyses; 2,365 (14%) received a transplant, 5,639 (34%) died before transplant, and 8,410 (51%) were administratively censored. Our final model characterized patients based on five broad patterns of weight change (BMI trajectories): "late BMI decline" (about 2 years after commencing hemodialysis); "rapid BMI decline" (immediately after commencing hemodialysis); "stable and normal/overweight BMI"; "stable and morbidly obese BMI"; or "increasing BMI." Mortality rates were highest among classes with declining BMI, and the timing of weight loss coincided with the timing of increases in mortality. Within the two stable BMI classes, death rates were slightly lower among the morbidly obese. CONCLUSIONS: The findings from this descriptive analysis suggest a paradoxical association between obesity and better survival. However, they also suggest that the shape of the BMI trajectory is important, with stable BMI trajectories being beneficial. Future research should be aimed at understanding the causes of weight changes during dialysis, to determine whether there could be strategies to improve patient survival.

UK and Irish Y-STR population data-A catalogue of variant alleles.

A total of 3128 Y-STR profiles from three UK and one Irish population have been analysed with the PowerPlex Y23 system and are reported here. Instances of haplotype sharing between apparently unrelated individuals were identified and further investigated with the use of the 5 additional markers within the Yfiler Plus kit, resulting in a reduction by 76% in the number of shared haplotypes. Furthermore, Yfiler Plus was also employed to verify locus deletions and duplications observed in Y23 genotypes while inconsistencies between the two kits were sequenced, revealing underlying Y23 primer binding site mutations in loci DYS392 and DYS576. Finally, the mechanism behind a previously reported population specific peak shift observed in DYS481 in South Asian samples has been evaluated and further investigated in a novel case of this phenomenon seen in a Black British individual featuring a different flanking region mutation.

On the shape and likelihood of oceanic rogue waves.

We consider the observation and analysis of oceanic rogue waves collected within spatio-temporal (ST) records of 3D wave fields. This class of records, allowing a sea surface region to be retrieved, is appropriate for the observation of rogue waves, which come up as a random phenomenon that can occur at any time and location of the sea surface. To verify this aspect, we used three stereo wave imaging systems to gather ST records of the sea surface elevation, which were collected in different sea conditions. The wave with the ST maximum elevation (happening to be larger than the rogue threshold 1.25H s) was then isolated within each record, along with its temporal profile. The rogue waves show similar profiles, in agreement with the theory of extreme wave groups. We analyze the rogue wave probability of occurrence, also in the context of ST extreme value distributions, and we conclude that rogue waves are more likely than previously reported; the key point is coming across them, in space as well as in time. The dependence of the rogue wave profile and likelihood on the sea state conditions is also investigated. Results may prove useful in predicting extreme wave occurrence probability and strength during oceanic storms.

Phase 1 Dose-Escalation Study of Pegylated Arginine Deiminase, Cisplatin, and Pemetrexed in Patients With Argininosuccinate Synthetase 1-Deficient Thoracic Cancers.

Purpose Pegylated arginine deiminase (ADI-PEG 20) depletes essential amino acid levels in argininosuccinate synthetase 1 (ASS1) -negative tumors by converting arginine to citrulline and ammonia. The main aim of this study was to determine the recommended dose, safety, and tolerability of ADI-PEG 20, cisplatin, and pemetrexed in patients with ASS1-deficient malignant pleural mesothelioma (MPM) or non-small-cell lung cancer (NSCLC). Patients and Methods Using a 3 + 3 + 3 dose-escalation study, nine chemotherapy-naïve patients (five MPM, four NSCLC) received weekly ADI-PEG 20 doses of 18 mg/m2, 27 mg/m2, or 36 mg/m2, together with pemetrexed 500 mg/m2 and cisplatin 75 mg/m2 which were given every three weeks (maximum of six cycles). Patients achieving stable disease or better could continue ADI-PEG 20 monotherapy until disease progression or withdrawal. Adverse events were assessed by Common Terminology Criteria for Adverse Events version 4.03, and pharmacodynamics and immunogenicity were also evaluated. Tumor response was assessed by Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1 for NSCLC and by modified RECIST criteria for MPM. Results No dose-limiting toxicities were reported; nine of 38 reported adverse events (all grade 1 or 2) were related to ADI-PEG 20. Circulating arginine concentrations declined rapidly, and citrulline levels increased; both changes persisted at 18 weeks. Partial responses were observed in seven of nine patients (78%), including three with either sarcomatoid or biphasic MPM. Conclusion Target engagement with depletion of arginine was maintained throughout treatment with no dose-limiting toxicities. In this biomarker-selected group of patients with ASS1-deficient cancers, clinical activity was observed in patients with poor-prognosis tumors. Therefore, we recommend a dose for future studies of weekly ADI-PEG 20 36 mg/m2 plus three-weekly cisplatin 75 mg/m2 and pemetrexed 500 mg/m2.

Arginine Deprivation With Pegylated Arginine Deiminase in Patients With Argininosuccinate Synthetase 1-Deficient Malignant Pleural Mesothelioma: A Randomized Clinical Trial.

IMPORTANCE: Preclinical studies show that arginine deprivation is synthetically lethal in argininosuccinate synthetase 1 (ASS1)-negative cancers, including mesothelioma. The role of the arginine-lowering agent pegylated arginine deiminase (ADI-PEG20) has not been evaluated in a randomized and biomarker-driven study among patients with cancer. OBJECTIVE: To assess the clinical impact of arginine depletion in patients with ASS1-deficient malignant pleural mesothelioma. DESIGN, SETTING, AND PARTICIPANTS: A multicenter phase 2 randomized clinical trial, the Arginine Deiminase and Mesothelioma (ADAM) study, was conducted between March 2, 2011, and May 21, 2013, at 8 academic cancer centers. Immunohistochemical screening of 201 patients (2011-2013) identified 68 with advanced ASS1-deficient malignant pleural mesothelioma. INTERVENTIONS: Randomization 2:1 to arginine deprivation (ADI-PEG20, 36.8 mg/m2, weekly intramuscular) plus best supportive care (BSC) or BSC alone. MAIN OUTCOMES AND MEASURES: The primary end point was progression-free survival (PFS) assessed by modified Response Evaluation Criteria in Solid Tumors (RECIST) (target hazard ratio, 0.60). Secondary end points were overall survival (OS), tumor response rate, safety, and quality of life, analyzed by intention to treat. We measured plasma arginine and citrulline levels, anti-ADI-PEG20 antibody titer, ASS1 methylation status, and metabolic response by 18F-fluorodeoxyglucose positron-emission tomography. RESULTS: Median (range) follow-up in 68 adults (median [range] age, 66 [48-83] years; 19% female) was 38 (2.5-39) months. The PFS hazard ratio was 0.56 (95% CI, 0.33-0.96), with a median of 3.2 months in the ADI-PEG20 group vs 2.0 months in the BSC group (P = .03) (absolute risk, 18% vs 0% at 6 months). Best response at 4 months (modified RECIST) was stable disease: 12 of 23 (52%) in the ADI-PEG20 group vs 2 of 9 (22%) in the BSC group (P = .23). The OS curves crossed, so life expectancy was used: 15.7 months in the ADI-PEG20 group vs 12.1 months in the BSC group (difference of 3.6 [95% CI, -1.0 to 8.1] months; P = .13). The incidence of symptomatic adverse events of grade at least 3 was 11 of 44 (25%) in the ADI-PEG20 group vs 4 of 24 (17%) in the BSC group (P = .43), the most common being immune related, nonfebrile neutropenia, gastrointestinal events, and fatigue. Differential ASS1 gene-body methylation correlated with ASS1 immunohistochemistry, and longer arginine deprivation correlated with improved PFS. CONCLUSIONS AND RELEVANCE: In this trial, arginine deprivation with ADI-PEG20 improved PFS in patients with ASS1-deficient mesothelioma. Targeting arginine is safe and warrants further clinical investigation in arginine-dependent cancers. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT01279967.

Description of artefacts in the PowerPlex Y23(®) system associated with excessive quantities of background female DNA.

Male on female sexual assault cases that involve azoospermic individuals, those where the male has penetrated but failed to ejaculate, those where there has been an extended interval between the sexual assault and sample collection or where there has been only digital penetration are often difficult to investigate by employing traditional autosomal STR testing. Such cases often involve minimal amounts of male DNA either being deposited initially or remaining after the passage of time. These cases are often further complicated by the presence of large amounts of female DNA compared to the relatively small amounts of male DNA on the intimate samples taken. Y-STR kits provide a solution that allows targeting of male DNA in a mixed male/female sample. However, large quantities of excess female DNA have the potential to generate non-specific artefact peaks. Here we characterise a number of previously reported artefacts observed in the PowerPlex(®) Y23 system. We demonstrate that some of these artefacts can impact on profile interpretation and that they are highly dependent on the levels of female DNA present. These artefacts have been characterised to assist practitioners with the interpretation of such samples.

Flow-noise and turbulence in two tidal channels.

Flow-noise resulting from oceanic turbulence and interactions with pressure-sensitive transducers can interfere with ambient noise measurements. This noise source is particularly important in low-frequency measurements (f < 100 Hz) and in highly turbulent environments such as tidal channels. This work presents measurements made in the Chacao Channel, Chile, and in Admiralty Inlet, Puget Sound, WA. In both environments, peak currents exceed 3 m/s and pressure spectral densities attributed to flow-noise are observed at frequencies up to 500 Hz. At 20 Hz, flow-noise exceeds mean slack noise levels by more than 50 dB. Two semi-empirical flow-noise models are developed and applied to predict flow-noise at frequencies from 20 to 500 Hz using measurements of current velocity and turbulence. The first model directly applies mean velocity and turbulence spectra while the second model relies on scaling arguments that relate turbulent dissipation to the mean velocity. Both models, based on prior formulations for infrasonic (f < 20 Hz) flow-noise, agree well with observations in Chacao Channel. In Admiralty Inlet, good agreement is shown only with the model that applies mean velocity and turbulence spectra, as the measured turbulence violates the scaling assumption in the second model.

Comparative analysis of human mitochondrial DNA from World War I bone samples by DNA sequencing and ESI-TOF mass spectrometry.

Mitochondrial DNA is commonly used in identity testing for the analysis of old or degraded samples or to give evidence of familial links. The Abbott T5000 mass spectrometry platform provides an alternative to the more commonly used Sanger sequencing for the analysis of human mitochondrial DNA. The robustness of the T5000 system has previously been demonstrated using DNA extracted from volunteer buccal swabs but the system has not been tested using more challenging sample types. For mass spectrometry to be considered as a valid alternative to Sanger sequencing it must also be demonstrated to be suitable for use with more limiting sample types such as old teeth, bone fragments, and hair shafts. In 2009 the Commonwealth War Graves Commission launched a project to identify the remains of 250 World War I soldiers discovered in a mass grave in Fromelles, France. This study characterises the performance of both Sanger sequencing and the T5000 platform for the analysis of the mitochondrial DNA extracted from 225 of these remains, both in terms of the ability to amplify and characterise DNA regions of interest and the relative information content and ease-of-use associated with each method.

Match criteria for human cell line authentication: where do we draw the line?

Continuous human cell lines have been used extensively as models for biomedical research. In working with these cell lines, researchers are often unaware of the risk of cross-contamination and other causes of misidentification. To reduce this risk, there is a pressing need to authenticate cell lines, comparing the sample handled in the laboratory to a previously tested sample. The American Type Culture Collection Standards Development Organization Workgroup ASN-0002 has developed a Standard for human cell line authentication, recommending short tandem repeat (STR) profiling for authentication of human cell lines. However, there are known limitations to the technique when applied to cultured samples, including possible genetic drift with passage. In our study, a dataset of 2,279 STR profiles from four cell banks was used to assess the effectiveness of the match criteria recommended within the Standard. Of these 2,279 STR profiles, 1,157 were grouped into sets of related cell lines-duplicate holdings, legitimately related samples or misidentified cell lines. Eight core STR loci plus amelogenin were used to unequivocally authenticate 98% of these related sets. Two simple match algorithms each clearly discriminated between related and unrelated samples, with separation between related samples at ≥80% match and unrelated samples at <50% match. A small degree of overlap was noted at 50-79% match, mostly from cell lines known to display variable STR profiles. These match criteria are recommended as a simple and effective way to interpret results from STR profiling of human cell lines.