Inter-Laboratory Evaluation of a Next-Generation Sequencing Panel for Acute Myeloid Leukemia

INTRODUCTION: Acute myeloid leukemia (AML) is a heterogeneous clonal disorder often associated with dismal overall survival. The clinical diversity of AML is reflected in the range of recurrent somatic mutations in several genes, many of which have a prognostic and therapeutic value. Targeted next-generation sequencing (NGS) of these genes has the potential for translation into clinical practice. In order to assess this potential, an inter-laboratory evaluation of a commercially available AML gene panel across three diagnostic centres in the UK and Ireland was performed.

METHODS: DNA from six AML patient samples was distributed to each centre and processed using a standardised workflow, including a common sequencing platform, sequencing chips and bioinformatics pipeline. A duplicate sample in each centre was run to assess inter- and intra-laboratory performance.

RESULTS: An average sample read depth of 2725X (range 629-5600) was achieved using six samples per chip, with some variability observed in the depth of coverage generated for individual samples and between centres. A total of 16 somatic mutations were detected in the six AML samples, with a mean of 2.7 mutations per sample (range 1-4) representing nine genes on the panel. 15/16 mutations were identified by all three centres. Allelic frequencies of the mutations ranged from 5.6 to 53.3 % (median 44.4 %), with a high level of concordance of these frequencies between centres, for mutations detected.

CONCLUSION: In this inter-laboratory comparison, a high concordance, reproducibility and robustness was demonstrated using a commercially available NGS AML gene panel and platform.

Understanding next generation sequencing in oncology: A guide for oncologists

DNA sequencing is now faster and cheaper than ever before, due to the development of next generation sequencing (NGS) technologies. NGS is now widely used in the research setting and is becoming increasingly utilised in clinical practice. However, due to evolving clinical commitments, increased workload and lack of training opportunities, many oncologists may be unfamiliar with the terminology and technology involved. This can lead to oncologists feeling daunted by issues such as how to interpret the vast amounts of data generated by NGS and the differences between sequencing platforms. This review article explains common concepts and terminology, summarises the process of DNA sequencing (including data analysis) and discusses the main factors to consider when deciding on a sequencing method. This article aims to improve oncologists' understanding of the most commonly used sequencing platforms and the ongoing challenges faced in expanding the use of NGS into routine clinical practice.

A metagenomic comparison of endemic viruses from broiler chickens with runting stunting syndrome and from normal birds

Runting-stunting syndrome (RSS) in broiler chickens is an enteric disease that causes significant economic losses to poultry producers worldwide due to elevated feed conversion ratios, decreased body weight during growth, and excessive culling. Of specific interest are the viral agents associated with RSS which have been difficult to fully characterise to date. Past research into the aetiology of RSS has implicated a wide variety of RNA and DNA viruses however, to date, no individual virus has been identified as the main agent of RSS and the current opinion is that it may be caused by a community of viruses, collectively known as the virome. This paper attempts to characterise the viral pathogens associated with 2 – 3 week old RSS-affected and unaffected broiler chickens using next-generation sequencing and comparative metagenomics. Analysis of the viromes identified a total of 20 DNA & RNA viral families, along with 2 unidentified categories, comprised of 31 distinct viral genera and 7 unclassified genera. The most abundant viral families identified in this study were the Astroviridae, Caliciviridae, Picornaviridae, Parvoviridae, Coronaviridae, Siphoviridae, and Myoviridae. This study has identified historically significant viruses associated with the disease such as chicken astrovirus, avian nephritis virus, chicken parvovirus, and chicken calicivirus along with relatively novel viruses such as chicken megrivirus and sicinivirus 1 and will help expand the knowledge related to enteric disease in broiler chickens, provide insights into the viral constituents of a healthy avian gut, and identify a variety of enteric viruses and viral communities appropriate for further study.

Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line

Here, we describe gene expression compositional assignment (GECA), a powerful, yet simple method based on compositional statistics that can validate the transfer of prior knowledge, such as gene lists, into independent data sets, platforms and technologies. Transcriptional profiling has been used to derive gene lists that stratify patients into prognostic molecular subgroups and assess biomarker performance in the pre-clinical setting. Archived public data sets are an invaluable resource for subsequent in silico validation, though their use can lead to data integration issues. We show that GECA can be used without the need for normalising expression levels between data sets and can outperform rank-based correlation methods. To validate GECA, we demonstrate its success in the cross-platform transfer of gene lists in different domains including: bladder cancer staging, tumour site of origin and mislabelled cell lines. We also show its effectiveness in transferring an epithelial ovarian cancer prognostic gene signature across technologies, from a microarray to a next-generation sequencing setting. In a final case study, we predict the tumour site of origin and histopathology of epithelial ovarian cancer cell lines. In particular, we identify and validate the commonly-used cell line OVCAR-5 as non-ovarian, being gastrointestinal in origin. GECA is available as an open-source R package.

Efficient Genotyping of KRAS Mutant Non-Small Cell Lung Cancer Using a Multiplexed Droplet Digital PCR Approach.

Droplet digital PCR (ddPCR) can be used to detect low frequency mutations in oncogene-driven lung cancer. The range of KRAS point mutations observed in NSCLC necessitates a multiplex approach to efficient mutation detection in circulating DNA. Here we report the design and optimisation of three discriminatory ddPCR multiplex assays investigating nine different KRAS mutations using PrimePCR™ ddPCR™ Mutation Assays and the Bio-Rad QX100 system. Together these mutations account for 95% of the nucleotide changes found in KRAS in human cancer. Multiplex reactions were optimised on genomic DNA extracted from KRAS mutant cell lines and tested on DNA extracted from fixed tumour tissue from a cohort of lung cancer patients without prior knowledge of the specific KRAS genotype. The multiplex ddPCR assays had a limit of detection of better than 1 mutant KRAS molecule in 2,000 wild-type KRAS molecules, which compared favourably with a limit of detection of 1 in 50 for next generation sequencing and 1 in 10 for Sanger sequencing. Multiplex ddPCR assays thus provide a highly efficient methodology to identify KRAS mutations in lung adenocarcinoma.

Challenges in molecular testing in non-small-cell lung cancer patients with advanced disease

Lung cancer diagnostics have progressed greatly in the previous decade. Development of molecular testing to identify an increasing number of potentially clinically actionable genetic variants, using smaller samples obtained via minimally invasive techniques, is a huge challenge. Tumour heterogeneity and cancer evolution in response to therapy means that repeat biopsies or circulating biomarkers are likely to be increasingly useful to adapt treatment as resistance develops. We highlight some of the current challenges faced in clinical practice for molecular testing of EGFR, ALK, and new biomarkers such as PDL1. Implementation of next generation sequencing platforms for molecular diagnostics in non-small-cell lung cancer is increasingly common, allowing testing of multiple genetic variants from a single sample. The use of next generation sequencing to recruit for molecularly stratified clinical trials is discussed in the context of the UK Stratified Medicine Programme and The UK National Lung Matrix Trial.

Microbial phylogenetic and functional responses within acidified wastewater communities exhibiting enhanced phosphate uptake

Acid stimulated accumulation of insoluble phosphorus within microbial cells is highly beneficial to wastewater treatment but remains largely unexplored. Using single cell analyses and next generation sequencing, the response of active polyphosphate accumulating microbial communities under conditions of enhanced phosphorus uptake under both acidic and aerobic conditions was characterised. Phosphorus accumulation activities were highest under acidic conditions (pH 5.5 > 8.5), where a significant positive effect on bioaccumulation was observed at pH 5.5 when compared to pH 8.5. In contrast to the Betaproteobacteria and Actinobacteria dominated enhanced biological phosphorus removal process, the functionally active polyP accumulators at pH 5.5 belonged to the Gammaproteobacteria, with key accumulators identified as members of the families Aeromonadaceae and Enterobacteriaceae. This study demonstrated a significant enrichment of key polyphosphate kinase and exopolyphosphatase genes within the community metagenome after acidification, concomitant with an increase in P accumulation kinetics.

Improving Smartphones Battery Life by Reducing Energy Waste of Background Applications

Smartphones have undergone a remarkable evolution over the last few years, from simple calling devices to full fledged computing devices where multiple services and applications run concurrently. Unfortunately, battery capacity increases at much slower pace, resulting as a main bottleneck for Internet connected smartphones. Several software-based techniques have been proposed in the literature for improving the battery life. Most common techniques include data compression, packet aggregation or batch scheduling, offloading partial computations to cloud, switching OFF interfaces (e.g., WiFi or 3G/4G) periodically for short intervals etc. However, there has been no focus on eliminating the energy waste of background applications that extensively utilize smartphone resources such as CPU, memory, GPS, WiFi, 3G/4G data connection etc. In this paper, we propose an Application State Proxy (ASP) that suppresses/stops the applications on smartphones and maintains their presence on any other network device. The applications are resumed/restarted on smartphones only in case of any event, such as a new message arrival. In this paper, we present the key requirements for the ASP service and different possible architectural designs. In short, the ASP concept can significantly improve the battery life of smartphones, by reducing to maximum extent the usage of its resources due to background applications.

Matrix and reservoir-type multipurpose vaginal rings for controlled release of dapivirine and levonorgestrel

A matrix-type silicone elastomer vaginal ring providing 28-day continuous release of dapivirine (DPV) - a lead candidate human immunodeficiency virus type 1 (HIV-1) microbicide compound - has recently demonstrated moderate levels of protection in two Phase III clinical studies. Here, next-generation matrix and reservoir-type silicone elastomer vaginal rings are reported for the first time offering simultaneous and continuous in vitro release of DPV and the contraceptive progestin levonorgestrel (LNG) over a period of between 60 and 180days. For matrix-type vaginal rings comprising initial drug loadings of 100, 150 or 200mg DPV and 0, 16 or 32mg LNG, Day 1 daily DPV release values were between 4132 and 6113μg while Day 60 values ranged from 284 to 454μg. Daily LNG release ranged from 129 to 684μg on Day 1 and 2-91μg on Day 60. Core-type rings comprising one or two drug-loaded cores provided extended duration of in vitro release out to 180days, and maintained daily drug release rates within much narrower windows (either 75-131μg/day or 37-66μg/day for DPV, and either 96-150μg/day or 37-57μg/day for LNG, depending on core ring configuration and ignoring initial lag release effect for LNG) compared with matrix-type rings. The data support the continued development of these devices as multi-purpose prevention technologies (MPTs) for HIV prevention and long-acting contraception.

Combustion Noise

Combustion noise is becoming increasingly important as a major noise source in aeroengines and ground based gas turbines. This is partially because advances in design have reduced the other noise sources, and partially because next generation combustion modes burn more unsteadily, resulting in increased external noise from the combustion. This review reports recent progress made in understanding combustion noise by theoretical, numerical and experimental investigations. We first discuss the fundamentals of the sound emission from a combustion region. Then the noise of open turbulent flames is summarized. We subsequently address the effects of confinement on combustion noise. In this case not only is the sound generated by the combustion influenced by its transmission through the boundaries of the combustion chamber, there is also the possibility of a significant additional source, the so-called ‘indirect’ combustion noise. This involves hot spots (entropy fluctuations) or vorticity perturbations produced by temporal variations in combustion, which generate pressure waves (sound) as they accelerate through any restriction at the exit of the combustor. We describe the general characteristics of direct and indirect noise. To gain further insight into the physical phenomena of direct and indirect sound, we investigate a simple configuration consisting of a cylindrical or annular combustor with a low Mach number flow in which a flame zone burns unsteadily. Using a low Mach number approximation, algebraic exact solutions are developed so that the parameters controlling the generation of acoustic, entropic and vortical waves can be investigated. The validity of the low Mach number approximation is then verified by solving the linearized Euler equations numerically for a wide range of inlet Mach numbers, stagnation temperature ratios, frequency and mode number of heat release fluctuations. The effects of these parameters on the magnitude of the waves produced by the unsteady combustion are investigated. In particular the magnitude of the indirect and direct noise generated in a model combustor with a choked outlet is analyzed for a wide range of frequencies, inlet Mach numbers and stagnation temperature ratios. Finally, we summarize some of the unsolved questions that need to be the focus of future research

Electric Field Effects on Graphene Materials

Understanding the effect of electric fields on the physical and chemical properties of two-dimensional (2D) nanostructures is instrumental in the design of novel electronic and optoelectronic devices. Several of those properties are characterized in terms of the dielectric constant which play an important role on capacitance, conductivity, screening, dielectric losses and refractive index. Here we review our recent theoretical studies using density functional calculations including van der Waals interactions on two types of layered materials of similar two-dimensional molecular geometry but remarkably different electronic structures, that is, graphene and molybdenum disulphide (MoS2). We focus on such two-dimensional crystals because of they complementary physical and chemical properties, and the appealing interest to incorporate them in the next generation of electronic and optoelectronic devices. We predict that the effective dielectric constant (ε) of few-layer graphene and MoS2 is tunable by external electric fields (E ext). We show that at low fields (E ext < 0.01 V/Å) ε assumes a nearly constant value ∼4 for both materials, but increases at higher fields to values that depend on the layer thickness. The thicker the structure the stronger is the modulation of ε with the electric field. Increasing of the external field perpendicular to the layer surface above a critical value can drive the systems to an unstable state where the layers are weakly coupled and can be easily separated. The observed dependence of ε on the external field is due to charge polarization driven by the bias, which show several similar characteristics despite of the layer considered. All these results provide key information about control and understanding of the screening properties in two-dimensional crystals beyond graphene and MoS2