A5025417621- Liver Diseases and Immunity
- Genetic Associations and Epidemiology
- Liver Disease Diagnosis and Treatment
- RNA modifications and cancer
- Genetic Mapping and Diversity in Plants and Animals
- Genetic and phenotypic traits in livestock
- Gallbladder and Bile Duct Disorders
- Molecular Biology Techniques and Applications
- Epigenetics and DNA Methylation
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Drug Transport and Resistance Mechanisms
- Genetic Syndromes and Imprinting
- Bioinformatics and Genomic Networks
- Pediatric Hepatobiliary Diseases and Treatments
Newcastle University
2018-2023
Transcriptome imputation has become a popular method for integrating genotype data with publicly available expression to investigate the potentially causal role of genes in complex traits. Here, we compare three approaches (PrediXcan, MetaXcan and FUSION) via application genome-wide association study (GWAS) Crohn's disease type 1 diabetes from Wellcome Trust Case Control Consortium. We investigate: (i) how results each approach other those standard GWAS analysis; (ii) variants models used by...
Abstract In transcriptome‐wide association studies (TWAS), gene expression values are predicted using genotype data and tested for with a phenotype. The power of this approach to detect associations relies, at least in part, on the accuracy prediction. Here we compare prediction six different methods—LASSO, Ridge regression, Elastic net, Best Linear Unbiased Predictor, Bayesian Sparse Mixed Model, Random Forests—by performing cross‐validation from Geuvadis Project. We also examine (a) sample...
As popularised by PrediXcan (and related methods), transcriptome-wide association studies (TWAS), in which gene expression is imputed from single-nucleotide polymorphism (SNP) genotypes and tested for with a phenotype, are popular approach investigating the role of complex traits. Like expression, DNA methylation an important biological process and, being under genetic regulation, may be imputable SNP genotypes. Here, we investigate prediction CpG levels genotype data to help elucidate...