Modeling SNP dependence

Genome graphs allow very general representations of genetic variation; depending on the model and implementation, variation at different length-scales (single nucleotide polymorphisms (SNPs), structural variants) and on different sequence backgrounds can be incorporated with different levels of transparency.

27p viarchimedes 26-01-2022 11 0   Download

The stabilization and three-dimensional modeling of mutant proteins were also determined by using the I-Mutant 2.0 and Project HOPE webservers, respectively. In total, 772 missense SNPs were found in the APAF1 gene from the NCBI dbSNP database, 18 SNPs of which were demonstrated to be deleterious or damaging. Of those, 13 SNPs had a decreasing effect on protein stability, while the other 5 SNPs had an increasing effect. Based on the modeling results, some dissimilarities of mutant type amino acids from wild-type amino acids such as size, charge, and hydrophobicity were revealed.

11p thiencuuchu 27-11-2021 12 3   Download

This study investigated if the allele effect of a given single nucleotide polymorphism (SNP) for crossbred performance in pigs estimated in a genomic prediction model differs depending on its breed-oforigin, and how these are related to estimated effects for purebred performance.

15p vitzuyu2711 29-09-2021 7 1   Download

The important property of the quantitative traits of model organisms is time-dependent. However, the methodology for investigating the genetic interaction network over time is still lacking. Our study aims to provide insights into the mechanistic basis of epistatic interactions affecting the phenotypes of model organisms.

9p visilicon2711 20-08-2021 8 1   Download

Identifying genetic variants associated with complex human diseases is a great challenge in genome-wide association studies (GWAS). Single nucleotide polymorphisms (SNPs) arising from genetic background are often dependent. The existing methods, i.e., local index of significance (LIS) and pooled local index of significance (PLIS), were both proposed for modeling SNP dependence and assumed that the whole chromosome follows a hidden Markov model (HMM).

12p viwyoming2711 16-12-2020 20 1   Download

Genome-wide association studies (GWASs) have been widely used to discover the genetic basis of complex phenotypes. However, standard single-SNP GWASs suffer from lack of power. In particular, they do not directly account for linkage disequilibrium, that is the dependences between SNPs (Single Nucleotide Polymorphisms).

24p viconnecticut2711 28-10-2020 10 1   Download