Winner's curse in rare variant analysis: effect size estimation bias depends on effect direction and the association method used.

For complex human traits, a large portion of genetic heritability remains unaccounted for beyond common genetic variants; therefore, estimating the contribution of rare variants (RVs) to the etiology of complex traits is of interest. Research in this domain has primarily focused on gene-based RV testing methods, in which information from multiple variants is combined to maximize statistical power in detecting genes associated with the trait of interest. However, after discovering an association, estimating individual effects becomes challenging due to sample size limitations.

Pan-cancer classification of single cells in the tumour microenvironment.

Single-cell RNA sequencing can reveal valuable insights into cellular heterogeneity within tumour microenvironments (TMEs), paving the way for a deep understanding of cellular mechanisms contributing to cancer. However, high heterogeneity among the same cancer types and low transcriptomic variation in immune cell subsets present challenges for accurate, high-resolution confirmation of cells' identities. Here we present scATOMIC; a modular annotation tool for malignant and non-malignant cells.

Recombination affects allele-specific expression of deleterious variants in human populations.

How the genetic composition of a population changes through stochastic processes, such as genetic drift, in combination with deterministic processes, such as selection, is critical to understanding how phenotypes vary in space and time. Here, we show how evolutionary forces affecting selection, including recombination and effective population size, drive genomic patterns of allele-specific expression (ASE). Integrating tissue-specific genotypic and transcriptomic data from 1500 individuals from two different cohorts, we demonstrate that ASE is less often observed in regions of low recombination, and loci in high or normal recombination regions are more efficient at using ASE to underexpress harmful mutations.

Psychosocial factors and cancer incidence (PSY-CA): Protocol for individual participant data meta-analyses.

Objectives: Psychosocial factors have been hypothesized to increase the risk of cancer. This study aims (1) to test whether psychosocial factors (depression, anxiety, recent loss events, subjective social support, relationship status, general distress, and neuroticism) are associated with the incidence of any cancer (any, breast, lung, prostate, colorectal, smoking-related, and alcohol-related); (2) to test the interaction between psychosocial factors and factors related to cancer risk (smoking, alcohol use, weight, physical activity, sedentary behavior, sleep, age, sex, education, hormone replacement therapy, and menopausal status) with regard to the incidence of cancer; and (3) to test the mediating role of health behaviors (smoking, alcohol use, weight, physical activity, sedentary behavior, and sleep) in the relationship between psychosocial factors and the incidence of cancer.

Methods: The psychosocial factors and cancer incidence (PSY-CA) consortium was established involving experts in the field of (psycho-)oncology, methodology, and epidemiology.

Interacting evolutionary pressures drive mutation dynamics and health outcomes in aging blood.

Age-related clonal hematopoiesis (ARCH) is characterized by age-associated accumulation of somatic mutations in hematopoietic stem cells (HSCs) or their pluripotent descendants. HSCs harboring driver mutations will be positively selected and cells carrying these mutations will rise in frequency. While ARCH is a known risk factor for blood malignancies, such as Acute Myeloid Leukemia (AML), why some people who harbor ARCH driver mutations do not progress to AML remains unclear.

Score tests for scale effects, with application to genomic analysis.

Tests for variance or scale effects due to covariates are used in many areas and recently, in genomic and genetic association studies. We study score tests based on location-scale models with arbitrary error distributions that allow incorporation of additional adjustment covariates. Tests based on Gaussian and Laplacian double generalized linear models are examined in some detail.

Aberrant expression impacts the pan-cancer genomic landscape.

The binding of PRDM9 to chromatin is a key step in the induction of DNA double-strand breaks associated with meiotic recombination hotspots; it is normally expressed solely in germ cells. We interrogated 1879 cancer samples in 39 different cancer types and found that is unexpectedly expressed in 20% of these tumors even after stringent gene homology correction. The expression levels of in tumors are significantly higher than those found in healthy neighboring tissues and in healthy nongerm tissue databases.

Prediction of acute myeloid leukaemia risk in healthy individuals.

The incidence of acute myeloid leukaemia (AML) increases with age and mortality exceeds 90% when diagnosed after age 65. Most cases arise without any detectable early symptoms and patients usually present with the acute complications of bone marrow failure. The onset of such de novo AML cases is typically preceded by the accumulation of somatic mutations in preleukaemic haematopoietic stem and progenitor cells (HSPCs) that undergo clonal expansion.

Testing Calibration of Cox Survival Models at Extremes of Event Risk.

Risk prediction models can translate genetic association findings for clinical decision-making. Most models are evaluated on their ability to discriminate, and the calibration of risk-prediction models is largely overlooked in applications. Models that demonstrate good discrimination in training datasets, if not properly calibrated to produce unbiased estimates of risk, can perform poorly in new patient populations.

Gene-by-environment interactions in urban populations modulate risk phenotypes.

Uncovering the interaction between genomes and the environment is a principal challenge of modern genomics and preventive medicine. While theoretical models are well defined, little is known of the G × E interactions in humans. We used an integrative approach to comprehensively assess the interactions between 1.

Cystic fibrosis gene modifier SLC26A9 modulates airway response to CFTR-directed therapeutics.

Cystic fibrosis is realizing the promise of personalized medicine. Recent advances in drug development that target the causal CFTR directly result in lung function improvement, but variability in response is demanding better prediction of outcomes to improve management decisions. The genetic modifier SLC26A9 contributes to disease severity in the CF pancreas and intestine at birth and here we assess its relationship with disease severity and therapeutic response in the airways.

A generalized Levene's scale test for variance heterogeneity in the presence of sample correlation and group uncertainty.

We generalize Levene's test for variance (scale) heterogeneity between k groups for more complex data, when there are sample correlation and group membership uncertainty. Following a two-stage regression framework, we show that least absolute deviation regression must be used in the stage 1 analysis to ensure a correct asymptotic χk-12/(k-1) distribution of the generalized scale (gS) test statistic. We then show that the proposed gS test is independent of the generalized location test, under the joint null hypothesis of no mean and no variance heterogeneity.

A Joint Location-Scale Test Improves Power to Detect Associated SNPs, Gene Sets, and Pathways.

Gene-based, pathway, and other multivariate association methods are motivated by the possibility of GxG and GxE interactions; however, accounting for such interactions is limited by the challenges associated with adequate modeling information. Here we propose an easy-to-implement joint location-scale (JLS) association testing framework for single-variant and multivariate analysis that accounts for interactions without explicitly modeling them. We apply the JLS method to a gene-set analysis of cystic fibrosis (CF) lung disease, which is influenced by multiple environmental and genetic factors.

Variants in Solute Carrier SLC26A9 Modify Prenatal Exocrine Pancreatic Damage in Cystic Fibrosis.

Objectives: To test the hypothesis that multiple constituents of the apical plasma membrane residing alongside the causal cystic fibrosis (CF) transmembrane conductance regulator protein, including known CF modifiers SLC26A9, SLC6A14, and SLC9A3, would be associated with prenatal exocrine pancreatic damage as measured by newborn screened (NBS) immunoreactive trypsinogen (IRT) levels.

Study Design: NBS IRT measures and genome-wide genotype data were available on 111 subjects from Colorado, 37 subjects from Wisconsin, and 80 subjects from France. Multiple linear regression was used to determine whether any of 8 single nucleotide polymorphisms (SNPs) in SLC26A9, SLC6A14, and SLC9A3 were associated with IRT and whether other constituents of the apical plasma membrane contributed to IRT.

Assessing the change in attitudes, knowledge, and perspectives of medical students towards chiropractic after an educational intervention.

Objective : We assessed the change in attitudes, knowledge, and perspectives of medical students towards chiropractic after a 1-hour educational intervention. Methods : A mixed-methods approach was used with a 52-item cross-sectional paper survey and 1 focus group of third-year medical students. The views of these medical students towards chiropractic were assessed previously in their second-year of medical school.

Evidence for a causal relationship between early exocrine pancreatic disease and cystic fibrosis-related diabetes: a Mendelian randomization study.

Circulating immunoreactive trypsinogen (IRT), a biomarker of exocrine pancreatic disease in cystic fibrosis (CF), is elevated in most CF newborns. In those with severe CF transmembrane conductance regulator (CFTR) genotypes, IRT declines rapidly in the first years of life, reflecting progressive pancreatic damage. Consistent with this progression, a less elevated newborn IRT measure would reflect more severe pancreatic disease, including compromised islet compartments, and potentially increased risk of CF-related diabetes (CFRD).

Differentiating intraprofessional attitudes toward paradigms in health care delivery among chiropractic factions: results from a randomly sampled survey.

Background: As health care has increased in complexity and health care teams have been offered as a solution, so too is there an increased need for stronger interprofessional collaboration. However the intraprofessional factions that exist within every profession challenge interprofessional communication through contrary paradigms. As a contender in the conservative spinal health care market, factions within chiropractic that result in unorthodox practice behaviours may compromise interprofessional relations and that profession's progress toward institutionalization.

Unraveling the complex genetic model for cystic fibrosis: pleiotropic effects of modifier genes on early cystic fibrosis-related morbidities.

The existence of pleiotropy in disorders with multi-organ involvement can suggest therapeutic targets that could ameliorate overall disease severity. Here we assessed pleiotropy of modifier genes in cystic fibrosis (CF). CF, caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, affects the lungs, liver, pancreas and intestines.

Retention of blinding at follow-up in a randomized clinical study using a sham-control cervical manipulation procedure for neck pain: secondary analyses from a randomized clinical study.

Objective: Participants in clinical trials of spinal manipulation have not been rigorously blinded to group assignment. This study reports on secondary analyses of the retention of participant blinding beyond the immediate posttreatment time frame following a single-session, randomized clinical study. A novel control cervical manipulation procedure that has previously been shown to be therapeutically inert was contrasted with a typical manipulation procedure.

The effect of a lumbar support pillow on lumbar posture and comfort during a prolonged seated task.

Background: Several risk factors exist for the development of low back pain, including prolonged sitting and flexed spinal curvature. Several investigators have studied lumbar support devices and spinal curvatures in sitting, however few have investigated a pain population and reported a quantitative measure of comfort. The purpose of the current project was to determine whether a lumbar support pillow, outfitted with a cut-out to accommodate the bulk of posterior pelvic soft tissue volume, is more effective than a standard chair in promoting a neutral spinal posture and improving subjective and objective measures of comfort in healthy individuals and patients with low back pain.

Self-rated disability, fear-avoidance beliefs, nonorganic pain behaviors are important mediators of ranges of active motion in chronic whiplash patients.

Purpose: The influence of self-rated disability and fear-avoidance beliefs on whiplash sufferers in their performance of active ranges of motion has not been studied well. We undertook a cross-sectional study to determine this.

Methods: Chronic whiplash subjects completed a standard clinical examination.