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Genetic influences on antisocial behaviour, problem substance use and schizophrenia: evidence from quantitative genetic and molecular genetic studies
Published in John C. Gunn, Pamela J. Taylor, Forensic Psychiatry, 2014
Pamela J Taylor, Marianne BM van den Bree, Nigel Williams, Terrie E Moffitt
Association analysis can be made more efficient by exploiting the population’s linkage disequilibrium at a region of interest, making it the method of choice for refining a region on the chromosome originally identified by linkage analysis. Linkage disequilibrium is not equally distributed across the genome. Instead, a large proportion of the genome falls into segments of strong linkage disequilibrium within which there are a limited number of haplotypes. A haplotype is a combination of alleles of closely linked loci on a chromosome that tend to be inherited together (Gabriel et al., 2002). It is possible to select a small number of informative single nucleotide polymorphisms (SNPs) which, when analysed, either individually or as haplotypes, will ‘tag’ a high proportion of the genetic variation (Johnson et al., 2001). Indirect linkage disequilibrium association mapping, therefore, typically requires a dense set of informative markers spanning the region of interest to be genotyped in a subset which is representative of the population being studied (typically 100 chromosomes). From this first stage analysis, a set of informative SNPs that ‘tag’ the full set are selected and then genotyped in the entire sample. Whilst such an approach does not test directly for a disease variant, the ‘tag’ SNPs will be likely to be highly correlated, either individually or as haplotypes, with such a variant.
A behavioral model for mapping the genetic architecture of gut-microbiota networks
Published in Gut Microbes, 2021
Libo Jiang, Xinjuan Liu, Xiaoqing He, Yi Jin, Yige Cao, Xiang Zhan, Christopher H. Griffin, Claudia Gragnoli, Rongling Wu
By treating each network index as a phenotype, we performed association mapping for the interaction networks. We identified 61 significant host genetic variants throughout the human genome which are responsible for the centrality indices of each network (Fig. S1). Because of their role in mediating microbial networks, we call these variants microbial network quantitative trait loci (mnQTLs). First, emergent properties that characterize the same network are under the control of different sets of mnQTLs, suggesting that each property reflects a different topological aspect of a network. Second, in general, no overlapping loci were detected for the four types of networks, from which we conjecture that each type of microbial interactions possesses its own genetic basis. It appears that more mnQTLs control mutualism, antagonism, and altruism than aggression. Third, no common loci were detected between two seasons for each network, indicating that the genetic control of microbial networks is season-dependent. We found that more loci are activated to affect mutualism and altruism in summer than winter, but no such difference was observed for antagonism and aggression mnQTLs.
Microsatellite variation of ESR1, ESR2, and AR in Serbian women with primary ovarian insufficiency
Published in Climacteric, 2018
J. Li, R. Dalgleish, S. Vujovic, S. Dragojevic-Dikic, M. Ivanisevic, M. Ivovic, M. Tancic, J. Thompson, F. Al-Azzawi
Genotype-to-phenotype association mapping commonly utilizes two major classes of variants: single nucleotide polymorphisms and copy number variation. Microsatellites or short tandem repeats are informative genetic markers in the human genome and some might have biological functions depending upon their locations (coding regions or regulatory regions), so they are well established as a third major class of genotypic variation10. Considering that the initial follicular pool size and the rate of follicular depletion are associated with the age of menopause and given the fact that these germ cells express gonadal steroid receptors at various stages of development, it is plausible that genetic variants in sex hormone receptor genes involved in maintaining ovarian function could affect the risk of POI11.
Effects of the total dose and duration of γ-irradiation on the growth responses and induced SNPs of a Cymbidium hybrid
Published in International Journal of Radiation Biology, 2020
Sang Hoon Kim, Yeong Deuk Jo, Jaihyunk Ryu, Min Jeong Hong, Byoung-Cheorl Kang, Jin-Baek Kim
The recent development of next-generation sequencing technology has provided researchers with a cost-effective and rapid means to analyze DNA variants at the whole-genome level (Lee, Kim, et al. 2016; Tsai et al. 2017). For example, mutations, such as single base substitutions, deletions, and insertions, have been revealed by the whole-genome re-sequencing of Arabidopsis thaliana and rice (Hase et al. 2018; Cui et al. 2019). Genotyping-by-sequencing (GBS) technologies based on a next-generation sequencing platform are also applicable to studies of population genomics, association mapping, and large-scale detection of single nucleotide polymorphisms (SNPs) (Narum et al. 2013; Uitdewilligen et al. 2013; Ryu et al. 2019).