Genome-wide association studies in oesophageal adenocarcinoma and Barrett's oesophagus: a large-scale meta-analysis

Background: Esophageal adenocarcinoma (EA) is one of the fastest rising cancers in western countries. Barrett’s Esophagus (BE) is the premalignant precursor of EA. However, only a subset of BE patients develop EA, which complicates the clinical management in the absence of valid predictors. Genetic risk factors for BE and EA are incompletely understood. This study aimed to identify novel genetic risk factors for BE and EA.Methods: Within an international consortium of groups involved in the genetics of BE/EA, we performed the first meta-analysis of all genome-wide association studies (GWAS) available, involving 6,167 BE patients, 4,112 EA patients, and 17,159 representative controls, all of European ancestry, genotyped on Illumina high-density SNP-arrays, collected from four separate studies within North America, Europe, and Australia. Meta-analysis was conducted using the fixed-effects inverse variance-weighting approach. We used the standard genome-wide significant threshold of 5×10-8 for this study. We also conducted an association analysis following reweighting of loci using an approach that investigates annotation enrichment among the genome-wide significant loci. The entire GWAS-data set was also analyzed using bioinformatics approaches including functional annotation databases as well as gene-based and pathway-based methods in order to identify pathophysiologically relevant cellular pathways.Findings: We identified eight new associated risk loci for BE and EA, within or near the CFTR (rs17451754, P=4·8×10-10), MSRA (rs17749155, P=5·2×10-10), BLK (rs10108511, P=2·1×10-9), KHDRBS2 (rs62423175, P=3·0×10-9), TPPP/CEP72 (rs9918259, P=3·2×10-9), TMOD1 (rs7852462, P=1·5×10-8), SATB2 (rs139606545, P=2·0×10-8), and HTR3C/ABCC5 genes (rs9823696, P=1·6×10-8). A further novel risk locus at LPA (rs12207195, posteriori probability=0·925) was identified after re-weighting using significantly enriched annotations. This study thereby doubled the number of known risk loci. The strongest disease pathways identified (P<10-6) belong to muscle cell differentiation and to mesenchyme development/differentiation, which fit with current pathophysiological BE/EA concepts. To our knowledge, this study identified for the first time an EA-specific association (rs9823696, P=1·6×10-8) near HTR3C/ABCC5 which is independent of BE development (P=0·45).Interpretation: The identified disease loci and pathways reveal new insights into the etiology of BE and EA. Furthermore, the EA-specific association at HTR3C/ABCC5 may constitute a novel genetic marker for the prediction of transition from BE to EA. Mutations in CFTR, one of the new risk loci identified in this study, cause cystic fibrosis (CF), the most common recessive disorder in Europeans. Gastroesophageal reflux (GER) belongs to the phenotypic CF-spectrum and represents the main risk factor for BE/EA. Thus, the CFTR locus may trigger a common GER-mediated pathophysiology.

The Changing Face of Neolithic and Bronze Age Ireland: A Big Data Approach to the Settlement and Burial Records

This paper synthesizes and discusses the spatial and temporal patterns of archaeological sites in Ireland, spanning the Neolithic period and the Bronze Age transition (4300–1900 cal BC), in order to explore the timing and implications of the main changes that occurred in the archaeological record of that period. Large amounts of new data are sourced from unpublished developer-led excavations and combined with national archives, published excavations and online databases. Bayesian radiocarbon models and context- and sample-sensitive summed radiocarbon probabilities are used to examine the dataset. The study captures the scale and timing of the initial expansion of Early Neolithic settlement and the ensuing attenuation of all such activity—an apparent boom-and-bust cycle. The Late Neolithic and Chalcolithic periods are characterised by a resurgence and diversification of activity. Contextualisation and spatial analysis of radiocarbon data reveals finer-scale patterning than is usually possible with summed-probability approaches: the boom-and-bust models of prehistoric populations may, in fact, be a misinterpretation of more subtle demographic changes occurring at the same time as cultural change and attendant differences in the archaeological record.

A 'before and after' study of nursing students' self-assessed competence in identifying the needs of older patients in hospital using an educational workbook.

Background: A core component of nurse education is clinical practice in order to support the development of clinical skills and competence. Assessment and measurement of the clinical competence of nursing students is important to gauge their professional development and educational needs.

Aim: To evaluate the impact of an Older Persons’ Assessment Educational Workbook (OPAEW) and explore second year nursing students’ competence and their opinions and use of the workbook.

Methods: A ‘before and after’ pre-experimental design was undertaken with n=6 second year nursing students. Outcome measures were the Nursing Competencies Questionnaire and the Self-efficacy in Clinical Performance Scale. Content analysis of workbooks and a survey (n=5) of opinions regarding the workbook was undertaken.

Findings: Pre and post test results for the study (n=5) were tested to determine if there was a relationship between changes in the NCQ and SECP repeated measures and use of an OPAEW. Testing identified evidence of a statistically significant difference for both SECP measures (SECP28 p=0.043; SECP7 p=0.042), with no clear statistical evidence of a difference for the NCQ (p=0.08). A weak negative association (NCQ ρ=-0.600 p=0.285; SECP28 ρ=-0.300 p=0.624; SECP7 ρ=-0.205 p=0.741), was found indicating that those participants who scored the lowest scores at the start of the study, benefited most from the workbook.

Content analysis of the OPAEW (n=5) found that 3 of the 5 participants completed all components of the workbook, with a mean of 1051 words used (SD 281.8). Through the survey (n=5) students reported the workbook as a useful guide when undertaking a patient assessment.

Conclusions: The OPAEW showed potential as an intervention to support the development of nursing students’ competence in older person assessment skills.

A 'before and after' study of nursing students' self-assessed competence in identifying the needs of older patients in hospital using an educational workbook.

Background: A core component of nurse education is clinical practice in order to support the development of clinical skills and competence. Assessment and measurement of the clinical competence of nursing students is important to gauge their professional development and educational needs.

Aim: To evaluate the impact of an Older Persons’ Assessment Educational Workbook (OPAEW) and explore second year nursing students’ competence and their opinions and use of the workbook.

Methods: A ‘before and after’ pre-experimental design was undertaken with n=6 second year nursing students. Outcome measures were the Nursing Competencies Questionnaire and the Self-efficacy in Clinical Performance Scale. Content analysis of workbooks and a survey (n=5) of opinions regarding the workbook was undertaken.

Findings: Pre and post test results for the study (n=5) were tested to determine if there was a relationship between changes in the NCQ and SECP repeated measures and use of an OPAEW. Testing identified evidence of a statistically significant difference for both SECP measures (SECP28 p=0.043; SECP7 p=0.042), with no clear statistical evidence of a difference for the NCQ (p=0.08). A weak negative association (NCQ ρ=-0.600 p=0.285; SECP28 ρ=-0.300 p=0.624; SECP7 ρ=-0.205 p=0.741), was found indicating that those participants who scored the lowest scores at the start of the study, benefited most from the workbook.

Content analysis of the OPAEW (n=5) found that 3 of the 5 participants completed all components of the workbook, with a mean of 1051 words used (SD 281.8). Through the survey (n=5) students reported the workbook as a useful guide when undertaking a patient assessment.

Conclusions: The OPAEW showed potential as an intervention to support the development of nursing students’ competence in older person assessment skills.

Multivariate analysis of regional-scale geochemical data for environmental monitoring

A compositional multivariate approach is used to analyse regional scale soil geochemical data obtained as part of the Tellus Project generated by the Geological Survey Northern Ireland (GSNI). The multi-element total concentration data presented comprise XRF analyses of 6862 rural soil samples collected at 20cm depths on a non-aligned grid at one site per 2 km2. Censored data were imputed using published detection limits. Using these imputed values for 46 elements (including LOI), each soil sample site was assigned to the regional geology map provided by GSNI initially using the dominant lithology for the map polygon. Northern Ireland includes a diversity of geology representing a stratigraphic record from the Mesoproterozoic, up to and including the Palaeogene. However, the advance of ice sheets and their meltwaters over the last 100,000 years has left at least 80% of the bedrock covered by superficial deposits, including glacial till and post-glacial alluvium and peat. The question is to what extent the soil geochemistry reflects the underlying geology or superficial deposits. To address this, the geochemical data were transformed using centered log ratios (clr) to observe the requirements of compositional data analysis and avoid closure issues. Following this, compositional multivariate techniques including compositional Principal Component Analysis (PCA) and minimum/maximum autocorrelation factor (MAF) analysis method were used to determine the influence of underlying geology on the soil geochemistry signature. PCA showed that 72% of the variation was determined by the first four principal components (PC’s) implying “significant” structure in the data. Analysis of variance showed that only 10 PC’s were necessary to classify the soil geochemical data. To consider an improvement over PCA that uses the spatial relationships of the data, a classification based on MAF analysis was undertaken using the first 6 dominant factors. Understanding the relationship between soil geochemistry and superficial deposits is important for environmental monitoring of fragile ecosystems such as peat. To explore whether peat cover could be predicted from the classification, the lithology designation was adapted to include the presence of peat, based on GSNI superficial deposit polygons and linear discriminant analysis (LDA) undertaken. Prediction accuracy for LDA classification improved from 60.98% based on PCA using 10 principal components to 64.73% using MAF based on the 6 most dominant factors. The misclassification of peat may reflect degradation of peat covered areas since the creation of superficial deposit classification. Further work will examine the influence of underlying lithologies on elemental concentrations in peat composition and the effect of this in classification analysis.