Two-stage study designs combining genome-wide association studies, tag single-nucleotide polymorphisms, and exome sequencing: accuracy of genetic effect estimates

Genome-wide association studies (GWAS) test for disease-trait associations and estimate effect sizes at tag single-nucleotide polymorphisms (SNPs), which imperfectly capture variation at causal SNPs. Sequencing studies can examine potential causal SNPs directly; however, sequencing the whole genome or exome can be prohibitively expensive. Costs can be limited by using a GWAS to detect the associated region(s) at tag SNPs followed by targeted sequencing to identify and estimate the effect size of the causal variant. Genetic effect estimates obtained from association studies can be inflated because of a form of selection bias known as the winner’s curse. Conversely, estimates at tag SNPs can be attenuated compared to the causal SNP because of incomplete linkage disequilibrium. These two effects oppose each other. Analysis of rare SNPs further complicates our understanding of the winner’s curse because rare SNPs are difficult to tag and analysis can involve collapsing over multiple rare variants. In two-stage analysis of Genetic Analysis Workshop 17 simulated data sets, we find that selection at the tag SNP produces upward bias in the estimate of effect at the causal SNP, even when the tag and causal SNPs are not well correlated. The bias similarly carries through to effect estimates for rare variant summary measures. Replication studies designed with sample sizes computed using biased estimates will be under-powered to detect a disease-causing variant. Accounting for bias in the original study is critical to avoid discarding disease-associated SNPs at follow up

Factors associated with initiation and completion of the quadrivalent human papillomavirus vaccine series in an ontario cohort of grade 8 girls

Abstract Background Although over a hundred million dollars have been invested in offering free quadrivalent human papillomavirus (HPV) vaccination to young girls in Ontario, there continues to be very little information about its usage. In order to successfully guide future HPV vaccine programming, it is important to monitor HPV vaccine use and determine factors associated with use in this population. Methods Linking administrative health and immunization databases, we conducted a population-based, retrospective cohort study of girls eligible for Ontario's Grade 8 HPV vaccination program in Kingston, Frontenac, Lennox, and Addington. We determined the proportion of girls who initiated (at least one dose) and completed (all three doses) the vaccination series overall and according to socio-demographics, vaccination history, health services utilization, medical history, and program year. Multivariable logistic regression was used to estimate the strength of association between individual factors and initiation and completion, adjusted for all other factors. Results We identified a cohort of 2519 girls, 56.6% of whom received at least one dose of the HPV vaccine. Among vaccinated girls, 85.3% received all three doses. Vaccination history was the strongest predictor of initiation in that girls who received the measles-mumps-rubella, meningococcal C, and hepatitis B vaccines were considerably more likely to also receive the HPV vaccine (odds ratio 4.89; 95% confidence interval 4.04-5.92). Nevertheless, HPV vaccine uptake was more than 20% lower than that of these other vaccines. In addition, while series initiation was not influenced by income, series completion was. In particular, girls of low income were the least likely to receive all three indicated doses of the HPV vaccine (odds ratio 0.45; 95% confidence interval 0.28-0.72). Conclusions The current low level of HPV vaccine acceptance in Kingston, Frontenac, Lennox, and Addington will likely have important implications in terms of the health benefits and cost-effectiveness of its publicly funded program. We identified important factors associated with series initiation and completion that should be considered in efforts to improve HPV vaccine use in this population

Intravaginal and Menstrual Practices among Women Working in Food and Recreational Facilities in Mwanza, Tanzania: Implications for Microbicide Trials

Intravaginal and menstrual practices may potentially influence results of trials of microbicides for HIV prevention through effects on the vaginal environment and on adherence to microbicide and placebo products. As part of the feasibility study for the Microbicides Development Programme Phase 3 trial of a vaginal microbicide in Mwanza, a variety of quantitative and qualitative methods were used to describe these practices, associations with behaviour and underlying social norms among women working in food and recreational facilities. Intravaginal cleansing by inserting fingers and either water alone or soap and water was thought necessary to remove “uchafu” (dirt), referring to vaginal secretions, including menstrual blood and post-coital discharge. Vaginal cleansing was carried out within 2 hours after 45% of sex acts. Sexual enhancement practices were less common. Intravaginal and menstrual practices and associated behaviours and demographic factors should be measured and monitored throughout microbicide trials to enable analyses of their impacts on microbicide effectiveness

Colorectal cancer screening, perceived discrimination, and low-income and trust in doctors: a survey of minority patients

<p>Abstract</p> <p>Background</p> <p>Completion of colorectal cancer (CRC) screening testing is lower among low-income and minority groups than the population as a whole. Given the multiple cancer screening health disparities known to exist within the U.S., this study investigated the relationship between perceived discrimination, trust in most doctors, and completion of Fecal Occult Blood Testing (FOBT) among a low-income, minority primary care population in an urban setting.</p> <p>Methods</p> <p>We recruited a convenience sample of adults over age 40 (n = 282) from a federally qualified community health center (70% African American). Participants completed a survey which included measures of trust in most doctors, perceived discrimination, demographics and report of cancer screening.</p> <p>Results</p> <p>Participants reported high levels of trust in most doctors, regardless of sex, race, education or income. High trust was associated with low perceived discrimination (p < 0.01). The trend was for older participants to express more trust (p = 0.09) and less perceived discrimination (p < 0.01). Neither trust nor discrimination was associated with race or education. Trust was higher among participants over 50 who were up-to-date on FOBT screening vs. those who were not (31 vs. 29 (median), p < 0.05 by T-test). Among those over 50, up-to-date FOBT screening was nearly associated with high trust (p < 0.06; 95% CI 0.99, 1.28) and low perceived discrimination (p < 0.01; 95% CI 0.76, 0.96). Nevertheless, in multivariate-modeling, age and income explained FOBT completion better than race, trust and discrimination.</p> <p>Conclusion</p> <p>Perceived discrimination was related to income, but not race, suggesting that discrimination is not unique to minorities, but common to those in poverty. Since trust in most doctors trended toward being related to age, FOBT screening could be negatively influenced by low trust and perceived discrimination in health care settings. A failure to address these issues in middle-aged, low income individuals could exacerbate future disparities in CRC screening.</p

Testicular cancer: a longitudinal pilot study on stress response symptoms and quality of life in couples before and after chemotherapy

Goals of work: The current study was designed to longitudinally examine stress response symptoms (SRS) and quality of life (QoL) in couples confronted with disseminated testicular cancer. The objectives were to examine couples' patterns of adjustment over time and possible differences in adjustment between the patient and his partner.Materials and methods: Couples completed the Impact of Event Scale and the QoL subscales physical functioning, social functioning, and mental health of the RAND-36 before chemotherapy (T1), after completion of chemotherapy (T2), and 1 year later (T3). Results: Before chemotherapy 26% of the patients and 50% of partners reported clinically elevated levels of SRS. Patients reported lower physical and social functioning at T2 compared to T1 and T3. Partners reported an improvement in social functioning over the year and no changes in physical functioning or mental health. No relationships between patients and partners' functioning were found. One year after diagnosis, QoL of patients and partners was similar to that of reference groups, and patients even reported better physical functioning than the reference group. SRS of patients and partners were negatively related at T1, and patients and partners' social functioning were positively related at T2. Conclusions: According to stress response levels, the period before the start of chemotherapy was most stressful for couples. Adjustment patterns differ between testicular cancer patients and their partners with patients reporting lowered QoL after completion of chemotherapy. QoL of couples returned to normal levels 1 year after diagnosis. The effect of disseminated testicular cancer on the QoL of patients and their partners seems to be temporary. A minority may need clinical attention for severe SRS

A Distinct Translation Initiation Mechanism Generates Cryptic Peptides for Immune Surveillance

MHC class I molecules present a comprehensive mixture of peptides on the cell surface for immune surveillance. The peptides represent the intracellular protein milieu produced by translation of endogenous mRNAs. Unexpectedly, the peptides are encoded not only in conventional AUG initiated translational reading frames but also in alternative cryptic reading frames. Here, we analyzed how ribosomes recognize and use cryptic initiation codons in the mRNA. We find that translation initiation complexes assemble at non-AUG codons but differ from canonical AUG initiation in response to specific inhibitors acting within the peptidyl transferase and decoding centers of the ribosome. Thus, cryptic translation at non-AUG start codons can utilize a distinct initiation mechanism which could be differentially regulated to provide peptides for immune surveillance

Quantifying the effects of temperature on mosquito and parasite traits that determine the transmission potential of human malaria

Malaria transmission is known to be strongly impacted by temperature. The current understanding of how temperature affects mosquito and parasite life history traits derives from a limited number of empirical studies. These studies, some dating back to the early part of last century, are often poorly controlled, have limited replication, explore a narrow range of temperatures, and use a mixture of parasite and mosquito species. Here, we use a single pairing of the Asian mosquito vector, An. stephensi and the human malaria parasite, P. falciparum to conduct a comprehensive evaluation of the thermal performance curves of a range of mosquito and parasite traits relevant to transmission. We show that biting rate, adult mortality rate, parasite development rate, and vector competence are temperature sensitive. Importantly, we find qualitative and quantitative differences to the assumed temperature-dependent relationships. To explore the overall implications of temperature for transmission, we first use a standard model of relative vectorial capacity. This approach suggests a temperature optimum for transmission of 29°C, with minimum and maximum temperatures of 12°C and 38°C, respectively. However, the robustness of the vectorial capacity approach is challenged by the fact that the empirical data violate several of the model's simplifying assumptions. Accordingly, we present an alternative model of relative force of infection that better captures the observed biology of the vector-parasite interaction. This model suggests a temperature optimum for transmission of 26°C, with a minimum and maximum of 17°C and 35°C, respectively. The differences between the models lead to potentially divergent predictions for the potential impacts of current and future climate change on malaria transmission. The study provides a framework for more detailed, system-specific studies that are essential to develop an improved understanding on the effects of temperature on malaria transmission

An insight into the sialome of Simulium guianense (DIPTERA:SIMulIIDAE), the main vector of River Blindness Disease in Brazil

<p>Abstract</p> <p>Background</p> <p>Little is known about the composition and function of the saliva in black flies such as <it>Simulium guianense</it>, the main vector of river blindness disease in Brazil. The complex salivary potion of hematophagous arthropods counteracts their host's hemostasis, inflammation, and immunity.</p> <p>Results</p> <p>Transcriptome analysis revealed ubiquitous salivary protein families--such as the Antigen-5, Yellow, Kunitz domain, and serine proteases--in the <it>S. guianense </it>sialotranscriptome. Insect-specific families were also found. About 63.4% of all secreted products revealed protein families found only in <it>Simulium</it>. Additionally, we found a novel peptide similar to kunitoxin with a structure distantly related to serine protease inhibitors. This study revealed a relative increase of transcripts of the SVEP protein family when compared with <it>Simulium vittatum </it>and <it>S. nigrimanum </it>sialotranscriptomes. We were able to extract coding sequences from 164 proteins associated with blood and sugar feeding, the majority of which were confirmed by proteome analysis.</p> <p>Conclusions</p> <p>Our results contribute to understanding the role of <it>Simulium </it>saliva in transmission of <it>Onchocerca volvulus </it>and evolution of salivary proteins in black flies. It also consists of a platform for mining novel anti-hemostatic compounds, vaccine candidates against filariasis, and immuno-epidemiologic markers of vector exposure.</p

A novel RING finger protein, Znf179, modulates cell cycle exit and neuronal differentiation of P19 embryonal carcinoma cells

Znf179 is a member of the RING finger protein family. During embryogenesis, Znf179 is expressed in a restricted manner in the brain, suggesting a potential role in nervous system development. In this report, we show that the expression of Znf179 is upregulated during P19 cell neuronal differentiation. Inhibition of Znf179 expression by RNA interference significantly attenuated neuronal differentiation of P19 cells and a primary culture of cerebellar granule cells. Using a microarray approach and subsequent functional annotation analysis, we identified differentially expressed genes in Znf179-knockdown cells and found that several genes are involved in development, cellular growth, and cell cycle control. Flow cytometric analyses revealed that the population of G0/G1 cells decreased in Znf179-knockdown cells. In agreement with the flow cytometric data, the number of BrdU-incorporated cells significantly increased in Znf179-knockdown cells. Moreover, in Znf179-knockdown cells, p35, a neuronal-specific Cdk5 activator that is known to activate Cdk5 and may affect the cell cycle, and p27, a cell cycle inhibitor, also decreased. Collectively, these results show that induction of the Znf179 gene may be associated with p35 expression and p27 protein accumulation, which lead to cell cycle arrest in the G0/G1 phase, and is critical for neuronal differentiation of P19 cells

Glutathione Precursor N-Acetyl-Cysteine Modulates EEG Synchronization in Schizophrenia Patients: A Double-Blind, Randomized, Placebo-Controlled Trial

Glutathione (GSH) dysregulation at the gene, protein, and functional levels has been observed in schizophrenia patients. Together with disease-like anomalies in GSH deficit experimental models, it suggests that such redox dysregulation can play a critical role in altering neural connectivity and synchronization, and thus possibly causing schizophrenia symptoms. To determine whether increased GSH levels would modulate EEG synchronization, N-acetyl-cysteine (NAC), a glutathione precursor, was administered to patients in a randomized, double-blind, crossover protocol for 60 days, followed by placebo for another 60 days (or vice versa). We analyzed whole-head topography of the multivariate phase synchronization (MPS) for 128-channel resting-state EEGs that were recorded at the onset, at the point of crossover, and at the end of the protocol. In this proof of concept study, the treatment with NAC significantly increased MPS compared to placebo over the left parieto-temporal, the right temporal, and the bilateral prefrontal regions. These changes were robust both at the group and at the individual level. Although MPS increase was observed in the absence of clinical improvement at a group level, it correlated with individual change estimated by Liddle's disorganization scale. Therefore, significant changes in EEG synchronization induced by NAC administration may precede clinically detectable improvement, highlighting its possible utility as a biomarker of treatment efficacy