Quantitative methods for evaluating association between multiple rare genetic variants and complex human traits

First, we propose two methods for aggregation of rare variants in data from Genome-wide Association Studies (GWAS), a weighted haplotype-based approach and an imputation-based approach, to test for the effect of rare variants with GWAS data. Both methods can incorporate external sequencing data when available. Our methods clearly show enhanced statistical power over existing methods for a wide range of population-attributable risk, percentage of disease-contributing rare variants, and proportion of rare alleles working in different directions. We thus demonstrate that the evaluation of rare variants with GWAS data is possible, particularly when public sequencing data are incorporated. Second, we present a systematic evaluation of multiple weighting schemes through a series of simulations intended to mimic large sequencing studies of a quantitative trait. We evaluate existing phenotype-independent and phenotype-dependent methods, as well as weights estimated by penalized regression. We find that the difference in power between phenotype-dependent schemes is negligible when high-quality functional annotations are available. When functional annotations are unavailable or incomplete, all methods lose power; however, the variable selection methods outperform the others at a cost of increased computational time. In the absence of highly accurate annotation, we recommend variable selection methods (which can be viewed as statistical annotation) on top of regions implicated by a phenotype-independent weighting scheme. Finally, we propose a method to apply the Sequence Kernel Association Test (SKAT), a similarity-based approach for rare variant association, to data from admixed populations by first estimating local ancestry for each variant. In simulations, we find that when the true causal alleles are causal only from only one ancestral population, our proposed approaches show a marked improvement in power over the original SKAT method. In real data, our results support the previously reported European-specific association and illustrate the increased statistical power of the proposed methods to find such associations.Doctor of Philosoph

Adolescent Opiate Exposure in the Female Rat Induces Subtle Alterations in Maternal Care and Transgenerational Effects on Play Behavior

The non-medical use of prescription opiates, such as Vicodin® and MSContin®, has increased dramatically over the past decade. Of particular concern is the rising popularity of these drugs in adolescent female populations. Use during this critical developmental period could have significant long-term consequences for both the female user as well as potential effects on her future offspring. To address this issue, we have begun modeling adolescent opiate exposure in female rats and have observed significant transgenerational effects despite the fact that all drugs are withdrawn several weeks prior to pregnancy. The purpose of the current set of studies was to determine whether adolescent morphine exposure modifies postpartum care. In addition, we also examined juvenile play behavior in both male and female offspring. The choice of the social play paradigm was based on previous findings demonstrating effects of both postpartum care and opioid activity on play behavior. The findings revealed subtle modifications in the maternal behavior of adolescent morphine-exposed females, primarily related to the amount of time females’ spend nursing and in non-nursing contact with their young. In addition, male offspring of adolescent morphine-exposed mothers (MOR-F1) demonstrate decreased rough and tumble play behaviors, with no significant differences in general social behaviors (i.e., social grooming and social exploration). Moreover, there was a tendency toward increased rough and tumble play in MOR-F1 females, demonstrating the sex-specific nature of these effects. Given the importance of the postpartum environment on neurodevelopment, it is possible that modifications in maternal–offspring interactions, related to a history of adolescent opiate exposure, plays a role in the observed transgenerational effects. Overall, these studies indicate that the long-term consequences of adolescent opiate exposure can impact both the female and her future offspring

Yes, The Government Should Tax Soft Drinks: Findings from a Citizens’ Jury in Australia

Taxation has been suggested as a possible preventive strategy to address the serious public health concern of childhood obesity. Understanding the public’s viewpoint on the potential role of taxation is vital to inform policy decisions if they are to be acceptable to the wider community. A Citizens’ Jury is a deliberative method for engaging the public in decision making and can assist in setting policy agendas. A Citizens’ Jury was conducted in Brisbane, Australia in May 2013 to answer the question: Is taxation on food and drinks an acceptable strategy to the public in order to reduce rates of childhood obesity? Citizens were randomly selected from the electoral roll and invited to participate. Thirteen members were purposively sampled from those expressing interest to broadly reflect the diversity of the Australian public. Over two days, participants were presented with evidence on the topic by experts, were able to question witnesses and deliberate on the evidence. The jurors unanimously supported taxation on sugar-sweetened drinks but generally did not support taxation on processed meats, snack foods and foods eaten/ purchased outside the home. They also supported taxation on snack foods on the condition that traffic light labelling was also introduced. Though they were not specifically asked to deliberate strategies outside of taxation, the jurors strongly recommended more nutritional information on all food packaging using the traffic light and teaspoon labelling systems for sugar, salt and fat content. The Citizens’ Jury suggests that the general public may support taxation on sugar-sweetened drinks to reduce rates of obesity in children. Regulatory reforms of taxation on sugar-sweetened drinks and improved labelling of nutritional information on product packaging were strongly supported by all members of the jury. These reforms should be considered by governments to prevent childhood obesity and the future burden on society from the consequences of obesity

Supporting International Ab Initio Flight Students Through English Language Training

Effective communication between ab initio flight students and their instructors is critical for efficient flight training; additionally, clear radio communications between student pilots and air traffic controllers is imperative for smooth and incident-free airport operations. During the Fall 2019 semester, Embry-Riddle Aeronautical University (ERAU) at Daytona Beach implemented a new semi-intensive eight-week course to improve the communicative skills of its international students who speak English as a second language. This presentation describes the cross-campus and cross-departmental collaboration that took place to implement this new course. The stages that will be described include (a) the pre-screening of the students using ERAU’s online, remotely administered English for Flight Training Assessment (EFTA)™, a project initiated by Daytona Beach’s Applied Aviation Sciences Department and the Embry-Riddle Language Institute, and (b) the employment of a curriculum specifically designed for ab-initio flight students based on flight training materials created by the Aviation English Specialists at ERAU, Worldwide. The presenters will describe the teaching approaches used during the course and provide insights about the challenges faced and lessons learned throughout the eight weeks. The topic of aviation-familiarity for English language instructors will be discussed along with plans for improving the course. The audience will leave with insights about how to directly support international ab initio flight students and understand how ERAU’s approach to effective English language training can serve as an exemplar for the industry

Increased reticulocytosis during infancy is associated with increased hospitalizations in sickle cell anemia patients during the first three years of life

Objective Among older children with sickle cell anemia, leukocyte counts, hemoglobin, and reticulocytosis have previously been suggested as disease severity markers. Here we explored whether these blood parameters may be useful to predict early childhood disease severity when tested in early infancy, defined as postnatal ages 60–180 days. Study Design Data from fifty-nine subjects who were followed at Children’s National Medical Center’s Sickle Cell Program for at least three years was retrospectively analyzed. Comparisons were made between white blood cell counts, hemoglobin and reticulocyte levels measured at ages 60–180 days and the clinical course of sickle cell anemia during infancy and childhood. Results A majority of subjects had demonstrable anemia with increased reticulocytosis. Only increased absolute reticulocyte levels during early infancy were associated with a significant increase in hospitalization during the first three years of life. Higher absolute reticulocyte counts were also associated with a markedly shorter time to first hospitalizations and a four-fold higher cumulative frequency of clinical manifestations over the first three years of life. No significant increase in white blood cell counts was identified among the infant subjects. Conclusions These data suggest that during early infancy, increased reticulocytosis among asymptomatic SCA subjects is associated with increased severity of disease in childhood

Association between circulating osteocalcin and cardiometabolic risk factors following a 4-week leafy green vitamin K-rich diet

© 2020 S. Karger AG, Basel. Copyright: All rights reserved. Background: Evidence suggests that lower serum undercarboxylated osteocalcin (ucOC) may be negatively associated with cardiometabolic health. We investigated whether individuals with a suppression of ucOC following an increase in dietary vitamin K1 exhibit a relative worsening of cardiometabolic risk factors. Materials and Methods: Men (n = 20) and women (n = 10) aged 62 ± 10 years participated in a randomized, controlled, crossover study. The primary analysis involved using data obtained from participants following a high vitamin K1 diet (HK; 4-week intervention of increased leafy green vegetable intake). High and low responders were defined based on the median percent reduction (30%) in ucOC following the HK diet. Blood pressure (resting and 24 h), arterial stiffness, plasma glucose, lipid concentrations, and serum OC forms were assessed. Results: Following the HK diet, ucOC and ucOC/tOC were suppressed more (p \u3c 0.01) in high responders (41 and 29%) versus low responders (12 and 10%). The reduction in ucOC and ucOC/tOC was not associated with changes in blood pressure, arterial stiffness, plasma glucose, or lipid concentrations in the high responders (p \u3e 0.05). Discussion/Conclusion: Suppression of ucOC via consumption of leafy green vegetables has no negative effects on cardiometabolic health, perhaps, in part, because of cross-talk mechanisms

Association between plasma neutrophil gelatinase-associated lipocalin and cardiac disease hospitalizations and deaths in older women

Background Neutrophil gelatinase-associated lipocalin ( NGAL ) or lipocalin 2 may promote atherosclerosis and plaque instability leading to increased risk of cardiac events. We investigated the relationships between plasma NGAL , cardiovascular disease biomarkers, and long-term cardiac events. Methods and Results The study population consisted of 1131 ambulant older white women (mean age 75 years) without clinical coronary heart disease ( CHD ) and measures of plasma NGAL in the Perth Longitudinal Study of Ageing Women with 14.5-year CHD and heart failure hospitalizations or death (events) captured using linked records. Over 14.5 years, 256 women had CHD events, while 118 had heart failure events. Per SD increase in log-transformed NGAL there was a 35% to 37% increase in relative hazards for CHD and heart failure events in unadjusted analyses, which remained significant after adjustment for conventional risk factors for CHD events (hazard ratio 1.29, 95% CI 1.13-1.48, P0.05). Women in the highest 2 quartiles of NGAL had higher relative hazards for CHD events compared with women in the lowest quartile hazard ratio 1.61, 95% CI 1.08-2.39, P=0.019 and hazard ratio 1.97, 95% CI 1.33-3.93, P=0.001, respectively. These associations were independent of high-sensitivity cardiac troponin I, homocysteine, and estimated renal function. NGAL correctly reclassified 1 in 4 women who sustained a CHD event up in risk and 1 in 10 women without CHD events down in risk. Conclusions NGAL was associated with increased risk of long-term CHD events, independent of conventional risk factors and biomarkers. These findings provide mechanistic insight into the role of NGAL with cardiac events

Serum Midkine, estimated glomerular filtration rate and chronic kidney disease-related events in elderly women: Perth Longitudinal Study of Aging Women

© 2020, The Author(s). Midkine (MDK), a heparin-binding growth factor cytokine, is involved in the pathogenesis of kidney diseases by augmenting leukocyte trafficking and activation. Animal models and small case control studies have implicated MDK as a pathological biomarker in chronic kidney diseases (CKD), however this is yet to be confirmed in prospective human studies. In a prospective study of 499 elderly, predominantly Caucasian women aged over 70 years the association between serum MDK collected in 1998, and renal function change and the risk of CKD-related hospitalisations and deaths at 5 and 14.5 years, respectively, was examined. Baseline serum MDK was not associated with 5-year change in estimated glomerular filtration rate using the CKD Epidemiology Collaboration creatinine and cystatin C equation (Standardised β = − 0.09, 95% confidence interval − 3.76–0.48, p = 0.129), 5-year rapid decline in renal function (odds ratio = 0.97, 95% confidence interval 0.46–2.02, p = 0.927) or the risk of 14.5-year CKD-related hospitalisations and deaths (hazard ratio = 1.27, 95% confidence interval.66–2.46, p = 0.470) before or after adjusting for major risk factors. In conclusion, in this cohort of elderly women with normal or mildly impaired renal function, serum MDK was not associated with renal function change or future CKD-related hospitalisations and deaths, suggesting that MDK may not be an early biomarker for progression of CKD

RBM47 regulates intestinal injury and tumorigenesis by modifying proliferation, oxidative response, and inflammatory pathways

RNA-binding protein 47 (RBM47) is required for embryonic endoderm development, but a role in adult intestine is unknown. We studied intestine-specific Rbm47-knockout mice (Rbm47-IKO) following intestinal injury and made crosses into ApcMin/+ mice to examine alterations in intestinal proliferation, response to injury, and tumorigenesis. We also interrogated human colorectal polyps and colon carcinoma tissue. Rbm47-IKO mice exhibited increased proliferation and abnormal villus morphology and cellularity, with corresponding changes in Rbm47-IKO organoids. Rbm47-IKO mice adapted to radiation injury and were protected against chemical-induced colitis, with Rbm47-IKO intestine showing upregulation of antioxidant and Wnt signaling pathways as well as stem cell and developmental genes. Furthermore, Rbm47-IKO mice were protected against colitis-associated cancer. By contrast, aged Rbm47-IKO mice developed spontaneous polyposis, and Rbm47-IKO ApcMin/+ mice manifested an increased intestinal polyp burden. RBM47 mRNA was decreased in human colorectal cancer versus paired normal tissue, along with alternative splicing of tight junction protein 1 mRNA. Public databases revealed stage-specific reduction in RBM47 expression in colorectal cancer associated independently with decreased overall survival. These findings implicate RBM47 as a cell-intrinsic modifier of intestinal growth, inflammatory, and tumorigenic pathways