Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Fun games and health: evaluating physical education related CPD provision in primary schools: the case of the Buntus programme

Thesis Summary: Continuous Professional Development (CPD) is essential for teachers to change practices. The teaching and context methodologies for teaching and facilitating effective PE-CPD programmes is a challenging endeavour. This study set out to evaluate PE related CPD provision in primary schools using the Buntus (Play & Multi-Sport) programme as a test case. Qualitative methods are useful in process evaluation for identifying user involvement and organisational pitfalls with the implementation. This study set out to investigate the extent to which this was implemented according to plan. Three stakeholders participated in this study, 14 Local Sports Partnership (LSP) tutors provided data through semi structured interviews. 17 group interviews (teachers) 15 group interviews (pupils) provided data from two counties. A general inductive approach was most appropriate for this study. Data were analysed inductively from units of information to submitting categories and themes in order to define questions that could be further explored. The findings state that PE was pupils\u27 favourite subject with evidence supporting the early influence of PE experiences on pupils\u27 PA behaviours; however adverse shortcomings left this subject relegated. Teachers believe PA was beneficial as a vehicle for PA; however, its inclusion reflected little educational value. The PE-CPD programme was considered to have positively affected teacher\u27s perceptions of PE (confidence in, knowledge of and enthusiasm for PE, and in turn, improved their practice (content ideas and inclusion). Key limitations included insufficient attention to specific pedagogical issues, the absence of follow-up support and a one-size-fits-all programme design. In conclusion, The perceptions of PE by teachers and pupils pertain this subject to be of little educational value. This programme positively contributed to teachers perceptions of PE; however, beyond this, its impact was limited by a range of factors highlighting the challenges of providing effective PE-CPD provision in schools.2017-05-1

Smoking, alcohol and drug use among young people.

This survey was carried out in 2002 as a follow-up to a study done in 1997. The survey aimed to document the prevalence and patterns of both licit and illict drug use in the post-primary population of the North Eastern Health Board (NEHB) region. It also aimed to present a profile of users and drugs being used and to compare the results to the 1997 survey, which would then provide useful information to assist in targeted health promotion campaigns. For the study 1,426 students from the ages of 12 to 19 inclusive from 24 post-primary schools in the NEHB completed a questionnaire. The study showed that the numbers of students that had ever smoked a cigarette had decreased from 57.1% in 1997 to 50.8%, with 18.2% classified as regular smokers compared with 30.7% in 1997. Regular smokers in 2002 smoked more daily than in 1997. 83.6% of regular smokers aged less than 18 buy their own cigarettes even though it is illegal to sell to them at this age. The lifetime prevalence for alcohol (ever having consumed a full alcoholic drink) was 71.3% in 2002, with 72.5% reported in 1997. The survey found 53.7% were regular drinkers (consuming one or more drinks per week) compared with 57.3% in 1997. 30% of drinkers reported having more than five drinks on a Saturday night compared with 27.1% in 1997; the number reporting more than 10 drinks increased from 3.5% in 1997 to 6.9% in 2002. The lifetime prevalence for illegal drugs was 41.2% in 2002 compared to 34.9% in 1997. 15.1% of those surveyed used drugs at least once in the last month and the drugs most commonly misused were cannabis (12.5%), glue/solvents (2.5%) and ecstasy (1.3%). There was little misuse of other illegal drugs

The localisation of the fast food industry in Ireland

For many years food as an academic discipline was ignored by academics in favour of more ‘serious’ topics such as poverty, unemployment and gender issues within the workplace. We as people now live in a consumer society were choice and variety is the norm. Our supermarkets are now filled with dozens of varieties of fruits, vegetables and meats which now mirror that of supermarkets in American the consumer capital of the world. However consumers have now become sceptical of the food industry and are worried how healthy food is on offer in supermarkets in light of food scares such as foot and mouth disease, BSE, and Salmonella. Since the beginning of this new century, a global obesity epidemic has come to dominate academic and medical interests. This was reflected in the popularity of Eric Schlosser’s Fast Food Nation (2000), Greg Critser’s Fat Land (2003) and Felicity Lawrence’s Not on the Label (2004).\ud The fast food industry and especially McDonald’s have come under severe criticism due to the high content of fat, sodium, and sugar in its products and the marketing strategies directed especially at children. McDonald’s and its golden arches have come to symbolise the rising levels of obesity in Irish society. This paper will not only discuss how McDonald’s has come to symbolise rising obesity levels, it will also discuss how a multinational like McDonald’s has come to symbolise broader sociological trends in society like the homogenization and dehumanization of the Irish landscape. The lack of non-union affiliation within the private service sector and how the globalisation of food is eroding our cultural identity and local democracy in what we eat. The research for this paper entailed interviews with different political activists groups like the Globalised Resistance Movement, the trade union SIPTU, members of the general public as well as the more traditional methods of research through medical journals and textbooks

Unilateral cilioretinal artery occlusion following cannabis use

There is a growing trend towards the decriminalization of cannabis and this is associated with its increased use over the past decade. Although a variety of adverse effects are attributed to its use, complications involving the eye are rare. We present the case of cilioretinal artery occlusion in a young man with no previous medical history. We discuss the management offered to him and present a review of the literature on this topic. Given the cilioretinal artery occlusion, medical management achieved an excellent result, with his best-corrected visual acuity improving to 6/12. Cilioretinal artery occlusions in healthy young individuals are extremely rare. The only risk factor identified in this patient was the use of cannabis on one occasion prior to his symptoms. There are no other cases in the literature that associate this complication with cannabis use and therefore it serves to raise awareness among the ophthalmic community