Statistical methods for the detection of single nucleotide polymorphisms (SNPs) using new generation genome sequencers

A single nucleotide polymorphism, or SNP, is a site of the genome where variation occurs within a population. Almost all SNPs have only two alleles (variants). Variations in the DNA sequences of humans can affect how humans develop diseases and respond to pathogens, chemicals, drugs, vaccines, and other agents. SNPs are also thought to be key enablers in realizing the concept of personalized medicine. The importance of SNPs also comes from their ability to in uence disease risk, drug efficacy and side-effects. Thus, there should be confidence in the methods for the detection of SNPs that a SNP found is not a sequencing error. In this work, a statistical method based on a likelihood ratio test has been considered to detect these SNPs. The effciency of this test has been compared with a threshold test using simulations. Results of the analysis of real genome sequence data are also presented

A likelihood ratio test for detection of single nucleotide polymorphisms (SNPs)

A single nucleotide polymorphism or SNP is a site of the genome where variation occurs within a population. Almost all SNPs have only two alleles (variants). In this work, we consider a statistical method based on a likelihood ratio test to detect these SNPs. We will also present some initial results of the analysis of real genome sequence data

Statistical methods for the detection of single nucleotide polymorphisms (SNPs) using new generation genome sequencers

Genome sequencing includes methods and technologies that are used for determining the order of nucleotides (A, T, C or G) along a DNA sequence. A single nucleotide polymorphism or SNP is a DNA sequence variation occurring when a single nucleotide in the genome differs within population members. Initially, we consider a particular site under a model where there are just two possible alleles. The following results can be then adapted to the case in which all four possible alleles (variants) may occur. The most common (rare) allele is termed the major (minor) allele respectively

Relation between obesity and depression using structural equation modelling

no abstract availabl

The impact of a novel digital sun protection campaign on sun‐related attitudes and behaviours of healthcare workers: A prospective observational study

Background: 13 000 cases of skin cancer are diagnosed annually in Ireland, with ultraviolet (UV) radiation exposure the strongest risk factor. Public health primary prevention campaigns focus on encouraging safe sun protective measures and skin cancer awareness. We designed a novel, digitally‐animated hospital‐based campaign targeting all aspects of sun‐ protective behaviour. Objectives: To explore the sun‐protective attitudes and behaviours of healthcare workers, and the effect of a digital hospital‐based campaign on these findings. Methods: This was a cross‐sectional prospective observational study involving hospital staff across the six hospitals that form the University of Limerick Hospital Group (ULHG). A two‐phase online survey, the first taking place before campaign launch, and the second upon campaign completion. The digital campaign was displayed across all hospital sites from June to September 2021. Surveys comprised questions on sun‐related attitudes and behaviours, including the internationally validated Sun Exposure Pro?tection Index (SEPI) questionnaire. Results: Eight hundred fifty‐seven staff members completed survey 1 and 704 completed survey 2; 90% in each were female; 79% were aged 25–54; 71% reported skin types I–III. Best sun‐protective habits pre‐campaign included sunscreen use and avoiding sunburn, while wearing hats, pro?tective clothing and seeking shade were least adopted. For 177 matched participants, there were small improvements in SEPI scores. SEPI Part 1 scores, reflecting improved risk behaviour, pre‐campaign had a median of 11 (IQR 7), and 11 (IQR 6) post campaign. SEPI Part 2 scores, reflecting readiness to adopt sun‐protective behaviours, improved from median 7 (IQR 8) to 6 (IQR 6). Post‐campaign, small improvements were seen across some individual sun‐protective behaviours and attitudes, particularly reducing time spent in the midday sun and on sun‐seeking holidays, and improved readiness to seek shade and reduce sunbathing; 79% of all respondents post‐campaign (n = 556) reported raised skin cancer awareness, and 65% (n = 458) said it influenced them to discuss sun protection with others.  Conclusions: Positive improvements in attitudes and behaviours related to sun protection were seen following the digital campaign in this population of healthcare workers. These improvements along with increased willingness to discuss sun protection with others, including patients, has the potential to further benefit wider society, and supports future digital health promotion initiatives. </p

Parent and child perceptions of physical activity with type 1 diabetes

Introduction Type 1 diabetes (T1D) is a lifelong illness that affects over 2500 children in Ireland. Management involves complex daily regimens including frequent blood glucose monitoring, pharmacotherapy, dietary management, and physical activity (PA). PA is an important modifiable lifestyle factor. Unfortunately, children with T1D remain physically inactive. Children with T1D face disease-specific barriers and facilitators to PA engagement. All aspects of T1D management for children are supported or supervised by parents. Thus, the purpose of this study was to examine parents’ and children’s perceptions of barriers and facilitators to PA engagement. Research design and methods 43 parent and child dyads participated. Parents completed a self-report survey. Children completed a modified version of the Physical Activity Questionnaire for Children (PAQ-C) that explored habitual PA patterns, perceived facilitators and barriers to PA engagement. Results 21 females, 22 males and their parents (36 mothers, 7 fathers) participated. 69% of males and 90% of females reported that having diabetes did affect their PA participation. 54% of males and 48% of females were insufficiently active based on their total PAQ-C score ( Conclusions This study demonstrates the potential influence of parents’ perceptions on PA engagement in children with T1D. Additional education is needed to support the promotion of PA for children with T1D. </p

Accuracy of the ActivPAL and Fitbit Charge 2 in measuring step count in Cystic Fibrosis

Background: Physical activity (PA) is important in Cystic Fibrosis (CF) management. Fitness wear?ables are becoming increasingly popular as measurement tools of PA; however, the accuracy of these devices should first be evaluated.Objective: The purpose of this study was to assess the accuracy of the ActivPAL and Fitbit Charge 2 as a measure of step count in Cystic Fibrosis.Methods: Twenty-one participants were recruited from an adult CF Center in Ireland for a single session of testing. Participants walked for 5 min at five pre-determined speeds in a controlled testing environment (2, 2.5, 3, 3.5 and 4 miles per hour on a treadmill) and at three self-selected speeds in a corridor (slow, medium, and fast). They concurrently wore an accelerometer (ActivPAL) and fitness wearable (Fitbit Charge 2), and both were compared to visual observations. Step count is the outcome being assessed.Results: The ActivPAL under-estimated step count by 0.63% across treadmill speeds and 1.1% across self-selected walking speeds. The Fitbit Charge 2 underestimated the step count by 2.97% across treadmill speeds and by 6.3% across self-selected walking speeds. Very strong correlations were found between the ActivPAL and visual observations (r: 0.93 to 0.99), while the Fitbit Charge 2 ranged from weak to very strong correlations when compared to visual observations (r: 0.34 to 0.84).Conclusion: The ActivPAL and Fitbit Charge 2 demonstrated acceptable validity for step count measurement in CF. These devices can be used for tracking PA during interventions in people with CF.</p

Move for Life an intervention for inactive adults aged 50 years and older: a cluster randomised feasibility trial

Background: Move for Life (MFL) is a theory-informed intervention that was developed to augment established physical activity (PA) programmes and enable inactive adults aged 50  years and older to be more active. This study examined the feasibility of MFL and sought to provide evidence of its potential for improving PA and associated health outcomes. Methods: A 3-arm cluster randomised feasibility trial compared MFL intervention, usual provision (UP) and control (CON) groups at baseline (T0), post-intervention (T1, at 8, 10 or 12- weeks) and 6-month follow up (T2). We used purposive sampling strategies to recruit participants according to characteristics of interest. Feasibility outcomes assessed recruitment, fidelity, adherence, retention and data completion rates based on pre-set criteria. Primary outcomes were accelerometer-based moderate-to-vigorous intensity PA (MVPA) and self-reported compliance with physical activity guidelines (PAGL). Secondary outcomes included light intensity PA (LiPA), standing time, sedentary time, body composition (adiposity), physical function and psychological well?being. We used linear mixed models (continuous outcomes) or generalized estimated equations (categorical outcomes) to estimate group differences over time in the study outcomes. Results: Progression criteria for feasibility outcomes were met, and 733 individuals were recruited. Considering a 6-month period (T0-T2), while self-reported compliance with PAGL increased in MFL relative to UP and CON and in UP relative to CON, standing time decreased in MFL relative to CON and sedentary time increased in the latter compared to UP. Waist circumference decreased in MFL relative to UP and CON. MFL outperformed UP in the Timed Up and Go Test while MFL and UP increased the distance covered in the Six-Minute Walk Test compared to CON. Psychological well-being increased in MFL relative to CON (all p  Conclusion: Findings show that MFL is feasible, while data are promising with regards to the potential of improving community PA programmes for adults aged 50 or more years.</p

Children’s Sport Participation and Physical Activity Study 2022

The Children’s Sport Participation and Physical Activity Study 2022 (CSPPA 2022) is an All-Island population research project that follows on from CSPPA in 2018 and 2010. A total of 8,881 school children and young people aged 10 to 19 on the island of Ireland were asked to report on various aspects related to sport participation and physical activity. CSPPA was a multi-centre study, undertaken by the University of Limerick, Dublin City University, University College Cork, and Ulster University. It was funded by Sport Ireland, Healthy Ireland and Sport Northern Ireland, with additional support from the Departments of Health and Education in the Republic of Ireland.</p

Findings from a pragmatic cluster randomised controlled feasibility trial of a music and dance programme for community dwelling older adults

Introduction Functional decline, chronic illness, reduced quality of life and increased healthcare utilisation are common in older adults. Evidence suggests music and dance can support healthy ageing in older adults. This study explored the feasibility, potential for effect and cost effectiveness of the Music and Movement for Health (MMH) programme among community-dwelling older adults using a pragmatic cluster-randomised, controlled feasibility trial design. Methods Community-dwelling adults aged 65 years or older were recruited to seven clusters in the Mid-West region of Ireland. Clusters were block randomised to either the MMH intervention or control. Primary feasibility outcomes included recruitment, retention, adherence, fidelity, and safety. Secondary outcomes measured physical activity, physical and cognitive performance, and psychosocial well-being, along with healthcare utilisation were assessed at baseline and after 12 weeks. Results The study successfully met feasibility targets, with recruitment (n = 100), retention (91 %), adherence (71 %), data completeness (92 %) and intervention fidelity (21 out of 24) all meeting predetermined criteria. Both groups exhibited an increase in self-reported physical activity and improved physical function. Participants in the intervention group scored consistently better in psychosocial measures compared to the control group at follow-up. The health economic analysis confirmed the feasibility of the methodology employed and points to the potential cost-effectiveness of the MMH relative to the control or no organised programme. Discussion and Implications The MMH intervention and study design were found to be feasible and acceptable with important findings to inform future evaluation of the clinical and cost-effectiveness of a definitive randomised controlled trial.</p