AIMC Topic: Alleles

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A deep learning method for HLA imputation and trans-ethnic MHC fine-mapping of type 1 diabetes.

Nature communications Mar 12, 2021
Conventional human leukocyte antigen (HLA) imputation methods drop their performance for infrequent alleles, which is one of the factors that reduce the reliability of trans-ethnic major histocompatibility complex (MHC) fine-mapping due to inter-ethn...
Humans Deep Learning Genome-Wide Association Study Genetic Predisposition to Disease Ethnicity Racial Groups Linkage Disequilibrium Major Histocompatibility Complex Histocompatibility Antigens Class II Genotype Diabetes Mellitus, Type 1 HLA Antigens Alleles Histocompatibility Antigens Class I
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Creating artificial human genomes using generative neural networks.

PLoS genetics Feb 4, 2021
Generative models have shown breakthroughs in a wide spectrum of domains due to recent advancements in machine learning algorithms and increased computational power. Despite these impressive achievements, the ability of generative models to create re...
HapMap Project Humans Markov Chains Neural Networks, Computer Genome, Human Machine Learning Population Algorithms Computer Simulation Chromosomes, Human, Pair 15 Databases, Factual Deep Learning Polymorphism, Single Nucleotide Databases, Genetic Alleles
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Artificial intelligence predicts the immunogenic landscape of SARS-CoV-2 leading to universal blueprints for vaccine designs.

Scientific reports Dec 23, 2020
The global population is at present suffering from a pandemic of Coronavirus disease 2019 (COVID-19), caused by the novel coronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The goal of this study was to use artificial intellige...
Algorithms SARS-CoV-2 Epitopes, T-Lymphocyte COVID-19 Vaccines Spike Glycoprotein, Coronavirus Humans Machine Learning Software Pandemics COVID-19 Drug Evaluation, Preclinical Proteomics Alleles Proteome Amino Acid Sequence Mutation Haplotypes HLA Antigens Immunogenicity, Vaccine
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Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools.

Scientific reports Nov 24, 2020
The outbreak of SARS-CoV-2 (2019-nCoV) virus has highlighted the need for fast and efficacious vaccine development. Stimulation of a proper immune response that leads to protection is highly dependent on presentation of epitopes to circulating T-cell...
Base Sequence Histocompatibility Antigens Class II Humans Spike Glycoprotein, Coronavirus Computational Biology HLA Antigens Alleles Histocompatibility Antigens Class I SARS-CoV-2 Epitopes, T-Lymphocyte Peptides Machine Learning COVID-19 Vaccines COVID-19
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Transfer learning enables prediction of CYP2D6 haplotype function.

PLoS computational biology Nov 2, 2020
Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic gene whose protein product metabolizes more than 20% of clinically used drugs. Genetic variations in CYP2D6 are responsible for interindividual heterogeneity in drug response that can lead to drug ...
Haplotypes Base Sequence Polymorphism, Genetic Pharmacogenomic Testing Cytochrome P-450 CYP2D6 Pharmaceutical Preparations Supervised Machine Learning Alleles Microsomes, Liver Humans Neural Networks, Computer Phenotype Computer Simulation Deep Learning Computational Biology DNA
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Machine learning discriminates a movement disorder in a zebrafish model of Parkinson's disease.

Disease models & mechanisms Oct 16, 2020
Animal models of human disease provide an system that can reveal molecular mechanisms by which mutations cause pathology, and, moreover, have the potential to provide a valuable tool for drug development. Here, we have developed a zebrafish model of...
Zebrafish Base Sequence Movement Dopaminergic Neurons Movement Disorders Gene Targeting Protein Deglycase DJ-1 Machine Learning Algorithms Brain Animals Gene Expression Profiling Disease Models, Animal Parkinson Disease Mutation Alleles
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Evaluating the informativeness of deep learning annotations for human complex diseases.

Nature communications Sep 17, 2020
Deep learning models have shown great promise in predicting regulatory effects from DNA sequence, but their informativeness for human complex diseases is not fully understood. Here, we evaluate genome-wide SNP annotations from two previous deep learn...
Deep Learning Genome-Wide Association Study Linkage Disequilibrium Genetic Predisposition to Disease Humans Alleles Polymorphism, Single Nucleotide Phenotype Genome, Human Models, Genetic Disease Molecular Sequence Annotation Histones
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Unsupervised Clustering of Missense Variants in HNF1A Using Multidimensional Functional Data Aids Clinical Interpretation.

American journal of human genetics Sep 9, 2020
Exome sequencing in diabetes presents a diagnostic challenge because depending on frequency, functional impact, and genomic and environmental contexts, HNF1A variants can cause maturity-onset diabetes of the young (MODY), increase type 2 diabetes ris...
Principal Component Analysis Gene Expression Registries Alleles Datasets as Topic United Kingdom Norway Exome Sequencing Mutation, Missense Diabetes Mellitus, Type 2 Genetic Predisposition to Disease Cluster Analysis Hepatocyte Nuclear Factor 1-alpha Unsupervised Machine Learning Adult Male Adolescent Child Humans Phenotype Female Young Adult
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Relation of vitamin D and BsmI variant with temporomandibular diseases in the Turkish population.

The British journal of oral & maxillofacial surgery Aug 28, 2020
Vitamin D (VD) levels and several variants in the vitamin D receptor (VDR) gene are associated with the occurrence of diseases of the bones and cartilage. The aim of this research was to study and compare the association of the BsmI variant in the VD...
Vitamin D Humans Receptors, Calcitriol Case-Control Studies Temporomandibular Joint Disorders Genetic Predisposition to Disease Alleles Genotype
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IConMHC: a deep learning convolutional neural network model to predict peptide and MHC-I binding affinity.

Immunogenetics Jun 24, 2020
Tumor-specific neoantigens are mutated self-peptides presented by tumor cell major histocompatibility complex (MHC) molecules and are necessary to elicit host's anti-cancer cytotoxic T cell responses. It could be specifically recognized by neoantigen...
Histocompatibility Antigens Class I Amino Acid Sequence Neural Networks, Computer Computer Simulation Humans Reproducibility of Results Peptides Deep Learning Protein Binding Antigens, Neoplasm Databases, Protein Alleles
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