KNN-MDR: a learning approach for improving interactions mapping performances in genome wide association studies

peer reviewedBackground Finding epistatic interactions in large association studies like genome-wide association studies (GWAS) with the nowadays-available large volume of genomic data is a challenging and largely unsolved issue. Few previous studies could handle genome-wide data due to the intractable difficulties met in searching a combinatorial explosive search space and statistically evaluating epistatic interactions given a limited number of samples. Our work is a contribution to this field. We propose a novel approach combining K-Nearest Neighbors (KNN) and Multi Dimensional Reduction (MDR) methods for detecting gene-gene interactions as a possible alternative to existing algorithms, e especially in situations where the number of involved determinants is high. After describing the approach, a comparison of our method (KNN-MDR) to a set of the other most performing methods (i.e., MDR, BOOST, BHIT, MegaSNPHunter and AntEpiSeeker) is carried on to detect interactions using simulated data as well as real genome-wide data. Results Experimental results on both simulated data and real genome-wide data show that KNN-MDR has interesting properties in terms of accuracy and power, and that, in many cases, it significantly outperforms its recent competitors. Conclusions The presented methodology (KNN-MDR) is valuable in the context of loci and interactions mapping and can be seen as an interesting addition to the arsenal used in complex traits analyses

Semen quality of stress negative Piétrain and Duroc boars in the tropics: the case of Vietnam

This study was carried out in Dong Hiep pig farm, North of Vietnam in order to evaluate the semen quality of stress negative Piétrain and Duroc boars. A total of 722 ejaculates from 13 homozygous (CC), 7 heterozygous (CT) stress negative Piétrain and 10 Duroc CC boars was collected between 2008 and 2012. The sperm quality was assessed on each ejaculate using ejaculate volume (VOL), spermatozoa motility (MO), sperm concentration (CO) and total number of spermatozoids (NT). Genetic type of boars, season, year and (season x year) as well as (genetic type x year) interactions were included in the model as fixed factors. The results show that the semen quality was influenced by all studied effects (p<0.05) except VOL for season (p=0.45) and season x year (p=0.55), and CO for genetic type (p=0.93). VOL and NT (291.74ml and 103.37×109spz) of Piétrain CC were higher than those (241.40ml and 84.58×109spz) of Piétrain CT and (228.05ml and 77.15×109spz) of Duroc (p<0.001) although the values of the 3 genetic groups are in the range of normal semen. MO, CO and NT tend to be higher in cold than in hot season (p<0.001). These results suggest that semen from Piétrain and Duroc boars could be used in tropical climatic conditions (particularly Piétrain CC) and that the semen quality could be improved through reduction of heat stress

Viral glycoprotein gp150 promotes sexual transmission of Murid Herpesvirus-4

Gammaherpesviruses are important pathogens in human and veterinary medicine. During co-evolution with their hosts, they developed many strategies allowing them to shed infectious particles in presence of immune response. Understanding these strategies is likely to be important to control infection. Interestingly, we recently observed that Murid herpesvirus 4 (MuHV-4), a gammaherpesvirus infecting laboratory mice, could be sexually transmitted between mice. This model offers therefore the opportunity to understand the mechanisms underlying natural transmission. Some of these mechanisms could rely on the glycoprotein 150 (gp150), which could limit virus neutralization and promote the release of infectious particles from cells. In this study, we tested therefore the importance of gp150 in the context of MuHV-4 sexual transmission. Briefly, female mice were infected with WT or gp150- strains expressing luciferase. They were imaged with an in vivo imaging system to follow infection. When lytic replication was observed in the genital tract, infected females were mated with naïve males to compare the capacity of transmission of the two strains. Our results show that, while the gp150- strain has no deficit in reaching and replicating in the female genital tract, it displays a major deficit of sexual transmission in comparison with WT virions. Interestingly, this deficit appears to reflect a deficit of virions release from vaginal epithelial cells. Altogether, our results show that, while gp150 is not required for efficient dissemination and maintenance of MuHV-4 within its host, it is essential for efficient transmission, by promoting the releasing of infectious particles from the mucosal cells