Gene hunting of the Genetic Analysis Workshop 16 rheumatoid arthritis data using rough set theory

We propose to use the rough set theory to identify genes affecting rheumatoid arthritis risk from the data collected by the North American Rheumatoid Arthritis Consortium. For each gene, we employ generalized dynamic reducts in the rough set theory to select a subset of single-nucleotide polymorphisms (SNPs) to represent the genetic information from this gene. We then group the study subjects into different clusters based on their genotype similarity at the selected markers. Statistical association between disease status and cluster membership is then studied to identify genes associated with rheumatoid arthritis. Based on our proposed approach, we are able to identify a number of statistically significant genes associated with rheumatoid arthritis. Aside from genes on chromosome 6, our identified genes include known disease-associated genes such as PTPN22 and TRAF1. In addition, our list contains other biologically plausible genes, such as ADAM15 and AGPAT2. Our findings suggest that ADAM15 and AGPAT2 may contribute to a genetic predisposition through abnormal angiogenesis and adipose tissue

Two-stage joint selection method to identify candidate markers from genome-wide association studies

The interaction among multiple genes and environmental factors can affect an individual's susceptibility to disease. Some genes may not show strong marginal associations when they affect disease risk through interactions with other genes. As a result, these genes may not be identified by single-marker methods that are widely used in genome-wide association studies. To explore this possibility in real data, we carried out a two-stage model selection procedure of joint single-nucleotide polymorphism (SNP) analysis to detect genes associated with rheumatoid arthritis (RA) using Genetic Analysis Workshop 16 genome-wide association study data. In the first stage, the genetic markers were screened through an exhaustive two-dimensional search, through which promising SNP and SNP pairs were identified. Then, LASSO was used to choose putative SNPs from the candidates identified in the first stage. We then use the RA data collected by the Wellcome Trust Case Control Consortium to validate the putative genetic factors. Balancing computational load and statistical power, this method detects joint effects that may fail to emerge from single-marker analysis. Based on our proposed approach, we not only replicated the identification of important RA risk genes, but also found novel genes and their epistatic effects on RA. To our knowledge, this is the first two-dimensional scan based analysis for a real genome-wide association study

The intriguing evolutionary dynamics of plant mitochondrial DNA

The mitochondrial genome of plants is-in every respect and for yet unclear reasons-very different from the well-studied one of animals. Thanks to next-generation sequencing technologies, Davila et al. precisely characterized the role played by recombination and DNA repair in controlling mitochondrial variations in Arabidopsis thaliana, thus opening new perspectives on the long-term evolution of this intriguing genome

Compliance with Positive Airway Pressure Treatment for Obstructive Sleep Apnea

ObjectivesPositive airway pressure (PAP) is considered a standard treatment for moderate-to-severe obstructive sleep apnea (OSA) patients. However, compliance with PAP treatment is suboptimal because of several types of discomfort experienced by patients. This study investigated compliance with PAP therapy, and affecting factors for such compliance, in OSA patients.MethodsWe performed a survey on 69 patients who engaged in PAP therapy between December 2006 and November 2007. After diagnostic polysomnography and manual titration, patients trialed PAP using the ResMed instrument and explored autoadjusting PAP (APAP), continuous PAP (CPAP), and flexible PAP (using expiratory pressure relief [EPR]) at least once every week for 1 month. Compliance measures were mean daily use (hr), percentage of days on which PAP was used, and percentage of days on which PAP was used for >4 hr. Data were obtained at night using the software Autoscan version 5.7® of the ResMed Inc. We obtained data on anthropometric (age, BMI, neck circumflex, Epworth sleepiness scale, Pittsburgh Sleep Quality Index, hypertension, alcohol intake), polysomnographic data (severity of apnea-hypopnea index [AHI], proportion of nonsupine sleep time, position dependence of sleep), PAP mode and AHI during PAP use for affecting factors.ResultsAfter 1 month, 41 of the 69 patients (59.4%) were pleased with PAP therapy and purchased instruments. Twenty-four patients (34.7%) used PAP for more than 3 months. The percentage of days on which PAP was used was statistically higher in patients with hypertension than in normotensive patients (P=0.003). There were negative correlations 1) between nonsupine position sleep time and percentage of days on which PAP was used (r=-0.424, P=0.039), and 2) between the AHI during PAP use and the percentage of days on which PAP was used for >4 hr (r=-0.443, P=0.030). There were no statistical differences between AHI, BMI, PAP pressure, or other measured parameters, on the one hand, and compliance, on the other.ConclusionThe affecting factors for PAP use were hypertension history, sleep posture (shorter nonsupine sleep time), and lower AHI during PAP use

Different approaches for dealing with rare variants in family-based genetic studies: application of a Genetic Analysis Workshop 17 problem

Rare variants are becoming the new candidates in the search for genetic variants that predispose individuals to a phenotype of interest. Their low prevalence in a population requires the development of dedicated detection and analytical methods. A family-based approach could greatly enhance their detection and interpretation because rare variants are nearly family specific. In this report, we test several distinct approaches for analyzing the information provided by rare and common variants and how they can be effectively used to pinpoint putative candidate genes for follow-up studies. The analyses were performed on the mini-exome data set provided by Genetic Analysis Workshop 17. Eight approaches were tested, four using the trait’s heritability estimates and four using QTDT models. These methods had their sensitivity, specificity, and positive and negative predictive values compared in light of the simulation parameters. Our results highlight important limitations of current methods to deal with rare and common variants, all methods presented a reduced specificity and, consequently, prone to false positive associations. Methods analyzing common variants information showed an enhanced sensibility when compared to rare variants methods. Furthermore, our limited knowledge of the use of biological databases for gene annotations, possibly for use as covariates in regression models, imposes a barrier to further research

Genetic Structure and Demographic History Should Inform Conservation: Chinese Cobras Currently Treated as Homogenous Show Population Divergence

An understanding of population structure and genetic diversity is crucial for wildlife conservation and for determining the integrity of wildlife populations. The vulnerable Chinese cobra (Naja atra) has a distribution from the mouth of the Yangtze River down to northern Vietnam and Laos, within which several large mountain ranges and water bodies may influence population structure. We combined 12 microsatellite loci and 1117 bp of the mitochondrial cytochrome b gene to explore genetic structure and demographic history in this species, using 269 individuals from various localities in Mainland China and Vietnam. High levels of genetic variation were identified for both mtDNA and microsatellites. mtDNA data revealed two main (Vietnam + southern China + southwestern China; eastern + southeastern China) and one minor (comprising only two individuals from the westernmost site) clades. Microsatellite data divided the eastern + southeastern China clade further into two genetic clusters, which include individuals from the eastern and southeastern regions, respectively. The Luoxiao and Nanling Mountains may be important barriers affecting the diversification of lineages. In the haplotype network of cytchrome b, many haplotypes were represented within a “star” cluster and this and other tests suggest recent expansion. However, microsatellite analyses did not yield strong evidence for a recent bottleneck for any population or genetic cluster. The three main clusters identified here should be considered as independent management units for conservation purposes. The release of Chinese cobras into the wild should cease unless their origin can be determined, and this will avoid problems arising from unnatural homogenization

The insulin-like growth factor system is modulated by exercise in breast cancer survivors: a systematic review and meta-analysis

Abbreviations: CI, Confidence interval; ELISA, Enzyme-linked immunosorbent assay; IGF, Insulin-like growth factors; IGFBP, Insulin-like growth factor binding protein; MD, Mean difference; PEDro, Physiotherapy evidence database; RCT, Randomized controlled trials; SD, Standard deviation.Background: Insulin-like growth factors (IGF´s) play a crucial role in controlling cancer cell proliferation, differentiation and apoptosis. Exercise has been postulated as an effective intervention in improving cancerrelated outcomes and survival, although its effects on IGF´s are not well understood. This meta-analysis aimed to determine the effects of exercise in modulating IGF´s system in breast cancer survivors. Methods: Databases of PuMed, EMBASE, Cochrane Central Register of Controlled Trials, EMBASE, ClinicalTrials. gov, SPORTDiscus, LILACS and Scopus were systematically searched up to November 2014. Effect estimates were calculated through a random-effects model of meta-analysis according to the DerSimonian and Laird method. Heterogeneity was evaluated with the I2 test. Risk of bias and methodological quality were evaluated using the PEDro score. Results: Five randomized controlled trials (n = 235) were included. Most women were post-menopausal. Highquality and low risk of bias were found (mean PEDro score = 6.2 ± 1). Exercise resulted in significant improvements on IGF-I, IGF-II, IGFBP-I, IGFBP-3, Insulin and Insulin resistance (P < 0.05). Non-significant differences were found for Glucose. Aerobic exercise improved IGF-I, IGFBP-3 and Insulin. No evidence of publication bias was detected by Egger´s test (p = 0.12). Conclusions: Exercise improved IGF´s in breast cancer survivors. These findings provide novel insight regarding the molecular effects of exercise on tumoral microenvironment, apoptosis and survival in breast cancer survivors

Molecular Phylogenetics of the Genus Neoconocephalus (Orthoptera, Tettigoniidae) and the Evolution of Temperate Life Histories

BACKGROUND:The katydid genus Neoconocephalus (25+ species) has a prominent acoustic communication system and occurs in large parts of the Neotropics and Nearctic. This group has been subject of numerous behavioral, physiological, and evolutionary studies of its acoustic communication system. Two distinct life histories occur in this group: The tropical life history incorporates multiple generations/year and direct egg development without environmental triggers. Temperate life history is characterized by overwintering in the egg stage, cold trigger of egg development, and one generation/year. This study reconstructs the phylogenetic relationships within the genus to (1) determine the evolutionary history of the temperate life history, and (2) to support comparative studies of evolutionary and physiological problems in this genus. METHODOLOGY/PRINCIPAL FINDINGS:We used Amplified Fragment Length Polymorphisms (AFLP), and sequences of two nuclear loci and one mitochondrial locus to reconstruct phylogenetic relationships. The analysis included 17 ingroup and two outgroup species. AFLP and mitochondrial data provided resolution at the species level while the two nuclear loci revealed only deeper nodes. The data sets were combined in a super-matrix to estimate a total evidence tree. Seven of the temperate species form a monophyletic group; however, three more temperate species were placed as siblings of tropical species. CONCLUSIONS/SIGNIFICANCE:Our analyses support the reliability of the current taxonomic treatment of the Neoconocephalus fauna of Caribbean, Central, and North America. Ancestral state reconstruction of life history traits was not conclusive, however at least four transitions between life histories occurred among our sample of species. The proposed phylogeny will strengthen conclusions from comparative work in this group