SuperFreq: Integrated mutation detection and clonal tracking in cancer.

Analysing multiple cancer samples from an individual patient can provide insight into the way the disease evolves. Monitoring the expansion and contraction of distinct clones helps to reveal the mutations that initiate the disease and those that drive progression. Existing approaches for clonal tracking from sequencing data typically require the user to combine multiple tools that are not purpose-built for this task. Furthermore, most methods require a matched normal (non-tumour) sample, which limits the scope of application. We developed SuperFreq, a cancer exome sequencing analysis pipeline that integrates identification of somatic single nucleotide variants (SNVs) and copy number alterations (CNAs) and clonal tracking for both. SuperFreq does not require a matched normal and instead relies on unrelated controls. When analysing multiple samples from a single patient, SuperFreq cross checks variant calls to improve clonal tracking, which helps to separate somatic from germline variants, and to resolve overlapping CNA calls. To demonstrate our software we analysed 304 cancer-normal exome samples across 33 cancer types in The Cancer Genome Atlas (TCGA) and evaluated the quality of the SNV and CNA calls. We simulated clonal evolution through in silico mixing of cancer and normal samples in known proportion. We found that SuperFreq identified 93% of clones with a cellular fraction of at least 50% and mutations were assigned to the correct clone with high recall and precision. In addition, SuperFreq maintained a similar level of performance for most aspects of the analysis when run without a matched normal. SuperFreq is highly versatile and can be applied in many different experimental settings for the analysis of exomes and other capture libraries. We demonstrate an application of SuperFreq to leukaemia patients with diagnosis and relapse samples

Frontiers of Seismology

Frontiers of Seismology was a wide-ranging, cross-disciplinary meeting held in Edinburgh in April this year. Susanne Sargeant, Lars Ottemöller, Brian Baptie, Andy Bell, Andrew Curtis and Ian Main join forces to give a flavour of the meeting and the new strengths it revealed in seismology in the UK

Effect of cadence selection on peak power and time of power production in elite BMX riders; a laboratory based study.

The aims of this study were to analyse the optimal cadence for peak power production and time to peak power in bicycle motocross (BMX) riders. Six male elite BMX riders volunteered for the study. Each rider completed 3 maximal sprints at a cadence of 80, 100, 120 and 140revs·min-1 on a laboratory Schoberer Rad Messtechnik (SRM) cycle ergometer in isokinetic mode. The riders’ mean values for peak power and time of power production in all three tests were recorded. The BMX riders produced peak power (1105±139W) at 100revs·min-1 with lower peak power produced at 80revs:min-1 (1060±69W, (F(2,15)=3.162; p=.266; η2 =0.960), 120revs·min-1 (1077±141W, (F(2,15)=4.348; p=.203; η2 =0.970) and 140revs·min-1 (1046±175W, (F(2,15)=12.350; p=0.077; η2 =0.989). The shortest time to power production was attained at 120revs·min-1 in 2.5±1.07s. Whilst a cadence of 80revs:min-1 (3.5±0.8s, (F(2,15)=2.667; p=.284; η2 =0.800) 100revs:min-1 (3.00±1.13s, (F(2,15)=24.832; p=.039; η2 =0.974) and 140revs:min-1 (3.50±0.88s, (F(2,15)=44.167; p=.006; η2 =0.967)) all recorded a longer time to peak power production. The results indicate that the optimal cadence for producing peak power output and reducing the time to peak power output are attained at comparatively low cadences for sprint cycling events. These findings could potentially inform strength and conditioning training to maximise dynamic force production and enable coaches to select optimal gear ratios

Standards for reporting clinical trials: The CONSORT statement for clinical trials in livestock. Application to food safety

Recently reviews of interventions studies in pre-harvest food safety have identified issues with lack of reporting of key methodological quality features and items necessary for interpretation and replication of trial findings. In human medicine, similar issues with the reporting of clinical trials were identified 10-15 years ago. This led to the publication of the CONsolidated Standards Of Reporting Trials (CONSORT) statement, which consists of a 22-item checklist of items that should be reported when publishing a clinical trial, a flow diagram to describe participant movement at all stages of a trial, and an explanation and elaboration document