Project description:This trial examines cancer communication within Hispanic social networks. Hispanics have the lowest colorectal cancer screening rate of any major ethnic group and health interventions are crucially needed among Hispanics. Patient decision aids are health communication interventions designed to provide patients with targeted health information and have shown to improve colorectal cancer screening rates among Hispanics. The goal of this study is to investigate, in a sample of Hispanics, how a colorectal cancer decision aid aimed at increasing individuals’ colorectal cancer screening behavior has effects on their alters’ intention to get screened for colorectal cancer.
Project description:Genome sequencing can offer critical insight into pathogen spread in viral outbreaks, but existing transmission inference methods use simplistic evolutionary models and only incorporate a portion of available genetic data. Here, we develop a robust evolutionary model for transmission reconstruction that tracks the genetic composition of within-host viral populations over time and the lineages transmitted between hosts. We confirm that our model reliably describes within-host variant frequencies in a dataset of 134,682 SARS-CoV-2 deep-sequenced genomes from Massachusetts, USA. We then demonstrate that our reconstruction approach infers transmissions more accurately than two leading methods on synthetic data, as well as in a controlled outbreak of bovine respiratory syncytial virus and an epidemiologically-investigated SARS-CoV-2 outbreak in South Africa. Finally, we apply our transmission reconstruction tool to 5,692 outbreaks among the 134,682 Massachusetts genomes. Our methods and results demonstrate the utility of within-host variation for transmission inference of SARS-CoV-2 and other pathogens, and provide an adaptable mathematical framework for tracking within-host evolution.
Project description:BackgroundSingle nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded from these analyses. Many investigators have addressed possible causes for departure from HWE, including genotyping errors, population admixture and segmental duplication. Recent large-scale surveys have revealed abundant structural variations in the human genome, including copy number variations (CNVs). This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE.ResultsWe performed a Bayesian analysis on the potential effect of copy number variation, segmental duplication and genotyping errors on the behavior of SNPs. Our results suggest that copy number variation is a major factor of HWE violation for SNPs with a small minor allele frequency, when the sample size is large and the genotyping error rate is 0~1%.ConclusionsOur study provides the posterior probability that a SNP falls in a CNV or a segmental duplication, given the observed allele frequency of the SNP, sample size and the significance level of HWE testing.
Project description:Analysis of Within-host Evolution of Plasmodium falciparum during treatment with Artemisinin Combination Therapies.This study looks and the evolutionary processes of Plasmodium falciparum within the human host during treatment with the ACT drugs.
Project description:To understand the effect of an adverse early life environment within the normal birth range we have utilised a non human primate model Macca fascicularis and employed microarray. We have identified 1973 genes which were differentially expressed in the three tissue types namely umbilical cord, neonatal liver, and skeletal muscle.