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Graphical Models in Genetics, Genomics, and Metagenomics
Published in Marloes Maathuis, Mathias Drton, Steffen Lauritzen, Martin Wainwright, Handbook of Graphical Models, 2018
If the eQTLs are located close to the genes they influence, they are called local eQTLs. Local eQTLs can act in cis by directly affecting only the expression of the gene that is on the same physical chromosome with it, as well as in trans, owing to changes in the function of a mediator [2]. In contrast, distant eQTLs refer to those that are located further away from the genes they influence and usually act in trans [37] (see Figure 21.1). As whole-genome sequencing data from different tissues/cell types become more accessible, there is a growing interest in integrative eQTL studies including joint analysis of eQTL mapping across multiple tissues for improved power [14] and Bayesian methods that combine external functional annotations with genetic association data for prioritizing causal variants in genome-wide association studies [16,29].
Application of an in silico approach identifies a genetic locus within ITGB2, and its interactions with HSPG2 and FGF9, to be associated with anterior cruciate ligament rupture risk
Published in European Journal of Sport Science, 2023
Senanile B. Dlamini, Colleen J. Saunders, Mary-Jessica N. Laguette, Andrea Gibbon, Junaid Gamieldien, Malcolm Collins, Alison V. September
Ligament injuries, such as anterior cruciate ligament (ACL) ruptures, are also one of the common lower limb injuries and the identification of additional genetic factors that modulate injury risk is an important step in elucidating the biological mechanism of injury risk. The aim of the current study was to identify candidate genes linked to both ACL ruptures and Achilles tendinopathy by using a biomedical knowledge discovery approach and to test these candidate genes in a genetic association study using a case–control study design for ACL rupture. The objectives included incorporating knowledge related to connective tissue and this involved the integration (i) of phenotypic features of ligament injuries into the biomedical knowledge graph previously developed specifically for tendon features by Saunders et al. (2016); (ii) relevant protein network pathways, known protein–protein interactions, specifically inflammatory signalling pathways.
The association of the ACTN3 R577X and ACE I/D polymorphisms with athlete status in football: a systematic review and meta-analysis
Published in Journal of Sports Sciences, 2021
Alexander B. T. McAuley, David C. Hughes, Loukia G. Tsaprouni, Ian Varley, Bruce Suraci, Thomas R. Roos, Adam J. Herbert, Adam L. Kelly
The collective results on the associations of the ACTN3 R577X and ACE I/D polymorphisms, with athletic performance, complicate the implications for sports which require both power and endurance related traits, such as football. Football is an intermittent sport which requires optimal utilisation of both the aerobic and anaerobic systems (Bangsbo et al., 2006; Buchheit et al., 2010; Dellal et al., 2011; Mallo et al., 2015); and as such, predicting whether a power or endurance-orientated allelic variant may be preferable is not straightforward. Therefore, genetic association studies began to investigate whether a power or endurance-orientated genotype was more important in football by analysing polymorphisms such as ACTN3 R577X and ACE I/D (Galeandro et al., 2017; Santiago et al., 2008; Ulucan et al., 2015). Moreover, studies began to assess if there was a difference between football players of various competitive playing levels (i.e. elite, non-elite; professional [PRO], non-professional [NP]) and controls (CON), in order to determine if ACTN3 R577X or ACE I/D were associated with athlete status (Coelho et al., 2018; Egorova et al., 2014; Honarpour et al., 2017). Currently, there is no general consensus on the importance of ACTN3 or ACE in footballers, with studies reporting positive, negative, and contrasting allelic associations (Coelho et al., 2018; Egorova et al., 2014; Galeandro et al., 2017; Honarpour et al., 2017; Santiago et al., 2008; Ulucan et al., 2015). This is most likely because each gene or genotype has a small contribution to sporting performance and is dependent on numerous inter-individual variations (e.g. ethnicity and competitive playing level) (Monnerat et al., 2019; Wang et al., 2013). As a result, studies require large homogenous sample sizes in order to have sufficient statistical power and demonstrate significant associations and replications (Sagoo et al., 2009; Wang et al., 2013). However, studies within football genomics have notoriously small sample sizes and many are heterogenic multi-sport studies; mainly due to the unique population and limited access available (McAuley et al., 2020). Therefore, to overcome the limitation of sample sizes and heterogeneity, a meta-analysis can be used to pool the results of single homogenous studies together (Sagoo et al., 2009). As such, the aim of this study was to assess if the ACTN3 R577X and/or ACE I/D polymorphism are associated with athlete status in football by conducting a systematic review and meta-analysis.