AIMC Topic: Genome-Wide Association Study

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A review of the use of tumour DNA methylation for breast cancer subtyping and prediction of outcomes.

Clinical epigenetics Jul 2, 2025
DNA methylation in breast tumours has been extensively studied and has provided valuable insights into the clinical heterogeneity of breast cancer. In this review, we summarise the current literature that has used DNA methylation markers to subtype b...
Humans Genome-Wide Association Study Machine Learning DNA Methylation Prognosis Receptors, Estrogen Female Breast Neoplasms Biomarkers, Tumor
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Identification of MEG3 and MAPK3 as potential therapeutic targets for osteoarthritis through multiomics integration and machine learning.

Scientific reports Jul 2, 2025
Knee osteoarthritis (KOA) is a prevalent degenerative joint disorder, yet its underlying molecular mechanisms remain puzzling. This study aimed to uncover the genes with a causal relationship to KOA using Mendelian randomization (MR), transcriptomic ...
Humans Machine Learning Gene Expression Profiling Genome-Wide Association Study Mendelian Randomization Analysis Osteoarthritis, Knee Quantitative Trait Loci Mitogen-Activated Protein Kinase 3 ROC Curve Multiomics RNA, Long Noncoding
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Neur-Ally: a deep learning model for regulatory variant prediction based on genomic and epigenomic features in brain and its validation in certain neurological disorders.

NAR genomics and bioinformatics Jun 13, 2025
Large-scale quantitative studies have identified significant genetic associations for various neurological disorders. Expression quantitative trait locus (eQTL) studies have shown the effect of single-nucleotide polymorphisms (SNPs) on the differenti...
Polymorphism, Single Nucleotide Autism Spectrum Disorder Epigenomics Brain Humans Deep Learning Nervous System Diseases Genome-Wide Association Study Quantitative Trait Loci
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Generative prediction of causal gene sets responsible for complex traits.

Proceedings of the National Academy of Sciences of the United States of America Jun 12, 2025
The relationship between genotype and phenotype remains an outstanding question for organism-level traits because these traits are generally . The challenge arises from complex traits being determined by a combination of multiple genes (or loci), whi...
Machine Learning Phenotype Gene Expression Profiling Transcriptome Humans Quantitative Trait Loci Multifactorial Inheritance Genome-Wide Association Study Genotype Models, Genetic
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Detecting genetic interactions with visible neural networks.

Communications biology Jun 5, 2025
Non-linear interactions among single nucleotide polymorphisms (SNPs), genes, and pathways play an important role in human diseases, but identifying these interactions is a challenging task. Neural networks are state-of-the-art predictors in many doma...
Genome-Wide Association Study Humans Polymorphism, Single Nucleotide Neural Networks, Computer Epistasis, Genetic Inflammatory Bowel Diseases Case-Control Studies
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Epistasis regulates genetic control of cardiac hypertrophy.

Nature cardiovascular research Jun 5, 2025
Although genetic variant effects often interact nonadditively, strategies to uncover epistasis remain in their infancy. Here we develop low-signal signed iterative random forests to elucidate the complex genetic architecture of cardiac hypertrophy, u...
Induced Pluripotent Stem Cells Connectin Magnetic Resonance Imaging Receptor, IGF Type 1 Heart Failure Ventricular Remodeling Myocytes, Cardiac Hypertrophy, Left Ventricular Epistasis, Genetic Deep Learning Genome-Wide Association Study Gene Regulatory Networks Humans Genetic Predisposition to Disease Aged Phenotype Male Female Middle Aged
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Performance of deep-learning-based approaches to improve polygenic scores.

Nature communications Jun 2, 2025
Polygenic scores, which estimate an individual's genetic propensity for a disease or trait, have the potential to become part of genomic healthcare. Neural-network based deep-learning has emerged as a method of intense interest to model complex, nonl...
Humans Neural Networks, Computer Gene-Environment Interaction Phenotype Multifactorial Inheritance Deep Learning Models, Genetic United Kingdom Linear Models Genome-Wide Association Study Linkage Disequilibrium Genetic Predisposition to Disease Polymorphism, Single Nucleotide
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Bridging Genomic Research Disparities in Osteoporosis GWAS: Insights for Diverse Populations.

Current osteoporosis reports May 24, 2025
PURPOSE OF REVIEW: Genome-wide association studies (GWAS) have significantly advanced osteoporosis research by identifying genetic loci associated with bone mineral density (BMD) and fracture risk. However, disparities persist due to the underreprese...
Genomics Genetic Predisposition to Disease Core Binding Factor Alpha 1 Subunit Asian People White People Gene-Environment Interaction Osteoporotic Fractures Machine Learning Bone Density Osteoporosis Genome-Wide Association Study Humans African People Low Density Lipoprotein Receptor-Related Protein-5
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Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions.

BMC genomics May 1, 2025
Plants exhibit extensive environment-dependent intraspecific metabolic variation, which likely plays a role in determining variation in whole plant phenotypes. However, much of the work seeking to use natural variation to link genes and transcript's ...
Genome, Plant Gene Expression Regulation, Plant Quantitative Trait Loci Genomics Metabolome Phenotype Plant Leaves Transcriptome Zea mays Genome-Wide Association Study
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Breaking down data silos across companies to train genome-wide predictions: A feasibility study in wheat.

Plant biotechnology journal Apr 20, 2025
Big data, combined with artificial intelligence (AI) techniques, holds the potential to significantly enhance the accuracy of genome-wide predictions. Motivated by the success reported for wheat hybrids, we extended the scope to inbred lines by integ...
Artificial Intelligence Phenotype Plant Breeding Genotype Triticum Genome-Wide Association Study Feasibility Studies Genomics Genome, Plant Polymorphism, Single Nucleotide
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