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

COVID-19-Related Vaccine Hesitancy among Community Hospitals’ Healthcare Workers in Singapore

COVID-19 has culminated in widespread infections and increased deaths over the last 3 years. In addition, it has also resulted in collateral economic and geopolitical tensions. Vaccination remains one of the cornerstones in the fight against COVID-19. Vaccine hesitancy must be critically evaluated in individual countries to promote vaccine uptake. We describe a survey conducted in three Singapore community hospitals looking at healthcare workers’ vaccine hesitancy and the barriers for its uptake. The online anonymous survey was conducted from March to July 2021 on all staff across three community hospital sites in SingHealth Singapore. The questionnaire was developed following a scoping review and was pilot tested and finalized into a 58-item instrument capturing data on demographics, contextual features, knowledge, attitudes, perceptions, and other vaccine-related factors in the vaccine hesitancy matrix. Logistic regression analysis was employed for all co-variates that are significant in univariate analysis. The response rate was 23.9%, and the vaccine hesitancy prevalence was 48.5% in the initial phase of the pandemic. On logistic regression analysis, only being female, a younger age, not having had a loved one or friend infected with COVID-19 and obtaining information from newspapers were associated with vaccine hesitancy in healthcare workers in Singapore community hospitals

COVID-19-Related Vaccine Hesitancy among Community Hospitals&rsquo; Healthcare Workers in Singapore

COVID-19 has culminated in widespread infections and increased deaths over the last 3 years. In addition, it has also resulted in collateral economic and geopolitical tensions. Vaccination remains one of the cornerstones in the fight against COVID-19. Vaccine hesitancy must be critically evaluated in individual countries to promote vaccine uptake. We describe a survey conducted in three Singapore community hospitals looking at healthcare workers&rsquo; vaccine hesitancy and the barriers for its uptake. The online anonymous survey was conducted from March to July 2021 on all staff across three community hospital sites in SingHealth Singapore. The questionnaire was developed following a scoping review and was pilot tested and finalized into a 58-item instrument capturing data on demographics, contextual features, knowledge, attitudes, perceptions, and other vaccine-related factors in the vaccine hesitancy matrix. Logistic regression analysis was employed for all co-variates that are significant in univariate analysis. The response rate was 23.9%, and the vaccine hesitancy prevalence was 48.5% in the initial phase of the pandemic. On logistic regression analysis, only being female, a younger age, not having had a loved one or friend infected with COVID-19 and obtaining information from newspapers were associated with vaccine hesitancy in healthcare workers in Singapore community hospitals

COVID-19 Vaccine Hesitancy—A Scoping Review of Literature in High-Income Countries

Vaccine hesitancy forms a critical barrier to the uptake of COVID-19 vaccine in high-income countries or regions. This review aims to summarize rates of COVID-19 hesitancy and its determinants in high-income countries or regions. A scoping review was conducted in Medline®, Embase®, CINAHL®, and Scopus® and was reported in accordance with the PRISMA-SCr checklist. The search was current as of March 2021. Studies which evaluated COVID-19 vaccine hesitancy and its determinants in high-income countries (US$12,536 or more GNI per capita in 2019) were included. Studies conducted in low, lower-middle, and upper-middle income countries or regions were excluded. Factors associated with vaccine hesitancy were grouped into four themes (vaccine specific, individual, group, or contextual related factors). Of 2237 articles retrieved, 97 articles were included in this review. Most studies were conducted in U.S. (n = 39) and Italy (n = 9). The rates of vaccine hesitancy across high-income countries or regions ranged from 7–77.9%. 46 studies (47.4%) had rates of 30% and more. Younger age, females, not being of white ethnicity and lower education were common contextual factors associated with increased vaccine hesitancy. Lack of recent history of influenza vaccination, lower self-perceived risk of contracting COVID-19, lesser fear of COVID-19, believing that COVID-19 is not severe and not having chronic medical conditions were most frequently studied individual/group factors associated with increased vaccine hesitancy. Common vaccine-specific factors associated with increased vaccine hesitancy included beliefs that vaccine are not safe/effective and increased concerns about rapid development of COVID-19 vaccines. Given the heterogeneity in vaccine hesitancy definitions used across studies, there is a need for standardization in its assessment. This review has summarized COVID-19 vaccine hesitancy determinants that national policymakers can use when formulating health policies related to COVID-19 vaccination

Public rental housing and its association with mortality – a retrospective, cohort study

Abstract Background Socioeconomic status (SES) is a well-established determinant of health status and home ownership is a commonly used composite indicator of SES. Patients in low-income households often stay in public rental housing. The association between public rental housing and mortality has not been examined in Singapore. Methods A retrospective, cohort study was conducted involving all patients who utilized the healthcare facilities under SingHealth Regional Health (SHRS) Services in Year 2012. Each patient was followed up for 5 years. Patients who were non-citizens or residing in a non-SHRS area were excluded from the study. Results A total of 147,004 patients were included in the study, of which 7252 (4.9%) patients died during the study period. The mean age of patients was 50.2 ± 17.2 years old and 7.1% (n = 10,400) of patients stayed in public rental housing. Patients who passed away had higher utilization of healthcare resources in the past 1 year and a higher proportion stayed in public rental housing (p < 0.001). They also had higher rates of co-morbidities such as hypertension, hyperlipidaemia and diabetes. (p < 0.001) After adjustment for demographic and clinical covariates, residence in public rental housing was associated with increased risk of all-cause mortality (Adjusted hazard ratio: 1.568, 95% CI: 1.469–1.673). Conclusion Public rental housing was an independent risk factor for all-cause mortality. More studies should be conducted to understand health-seeking behavior and needs of public rental housing patients, to aid policymakers in formulating better plans for improving their health outcomes

Outpatient primary and tertiary healthcare utilisation among public rental housing residents in Singapore

Abstract Background Globally, public housing is utilized to provide affordable housing for low-income households. Studies have shown an association between public housing and negative health outcomes. There is paucity of data pertaining to outpatient primary and tertiary healthcare resources utilization among public rental housing residents in Singapore. Methods A retrospective cohort study was performed, involving patients under the care of SingHealth Regional Health System (SHRS) in Year 2012. Healthcare utilization outcomes evaluated included number of outpatient primary and specialist care clinic visits, emergency department visits and hospitalization in Year 2011. Multivariate logistical analyses were used to examine the association between public rental housing and healthcare utilization. Results Of 147,105 patients, 10,400 (7.1%) patients stayed in public rental housing. There were more elderly (54.8 ± 18.0 vs 49.8 ± 17.1, p  0.05). However, it was associated with increased number of emergency department visits (OR: 2.41, 95% CI: 2.12–2.74) and frequent hospitalization (OR: 1.56, 95% CI: 1.33–1.83). Conclusion Residing in public rental housing was not associated with increased utilization of outpatient healthcare resources despite patients’ higher disease burden and frequency of emergency department visits and hospitalizations. Further research is required to elucidate their health seeking behaviours

Identifying heterogeneous health profiles of primary care utilizers and their differential healthcare utilization and mortality – a retrospective cohort study

Abstract Background Heterogeneity of population health needs and the resultant difficulty in health care resources planning are challenges faced by primary care systems globally. To address this challenge in population health management, it is critical to have a better understanding of primary care utilizers’ heterogeneous health profiles. We aimed to segment a population of primary care utilizers into classes with unique disease patterns, and to report the 1 year follow up healthcare utilizations and all-cause mortality across the classes. Methods Using de-identified administrative data, we included all adult Singapore citizens or permanent residents who utilized Singapore Health Services (SingHealth) primary care services in 2012. Latent class analysis was used to identify patient subgroups having unique disease patterns in the population. The models were assessed by Bayesian Information Criterion and clinical interpretability. We compared healthcare utilizations in 2013 and one-year all-cause mortality across classes and performed regression analysis to assess predictive ability of class membership on healthcare utilizations and mortality. Results We included 100,747 patients in total. The best model (k = 6) revealed the following classes of patients: Class 1 “Relatively healthy” (n = 58,213), Class 2 “Stable metabolic disease” (n = 26,309), Class 3 “Metabolic disease with vascular complications” (n = 2964), Class 4 “High respiratory disease burden” (n = 1104), Class 5 “High metabolic disease without complication” (n = 11,122), and Class 6 “Metabolic disease with multi-organ complication” (n = 1035). The six derived classes had different disease patterns in 2012 and 1 year follow up healthcare utilizations and mortality in 2013. “Metabolic disease with multiple organ complications” class had the highest healthcare utilization (e.g. incidence rate ratio = 19.68 for hospital admissions) and highest one-year all-cause mortality (hazard ratio = 27.97). Conclusions Primary care utilizers are heterogeneous and can be segmented by latent class analysis into classes with unique disease patterns, healthcare utilizations and all-cause mortality. This information is critical to population level health resource planning and population health policy formulation

Population segmentation of type 2 diabetes mellitus patients and its clinical applications - a scoping review

10.1186/s12874-021-01209-wBMC Medical Research Methodology2114