AIMC Topic: Genetic Variation

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Assigning function to SNPs: Considerations when interpreting genetic variation.

Seminars in cell & developmental biology Aug 24, 2021
Assigning function to single nucleotide polymorphisms (SNPs) to understand the mechanisms that link genetic and phenotypic variation and disease is an area of intensive research that is necessary to contribute to the continuing development of precisi...
Precision Medicine Polymorphism, Single Nucleotide Genetic Variation Humans Machine Learning
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Machine learning-based identification and characterization of 15 novel pathogenic SUOX missense mutations.

Molecular genetics and metabolism Aug 8, 2021
Isolated sulfite oxidase deficiency (ISOD) is a rare hereditary metabolic disease caused by absence of functional sulfite oxidase (SO) due to mutations of the SUOX gene. SO oxidizes toxic sulfite and sulfite accumulation is associated with neurologic...
Humans Machine Learning Brain Gene Frequency Infant, Newborn Mutation, Missense Genome Databases, Genetic Oxidoreductases Acting on Sulfur Group Donors Genetic Variation
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Application of the random forest algorithm to Streptococcus pyogenes response regulator allele variation: from machine learning to evolutionary models.

Scientific reports Jun 16, 2021
Group A Streptococcus (GAS) is a globally significant bacterial pathogen. The GAS genotyping gold standard characterises the nucleotide variation of emm, which encodes a surface-exposed protein that is recombinogenic and under immune-based selection ...
Regulon Genetic Variation Streptococcus pyogenes Genes, Bacterial Bacterial Outer Membrane Proteins Antigens, Bacterial Genome, Bacterial Bacterial Proteins Alleles Streptococcal Infections Algorithms Carrier Proteins Humans Evolution, Molecular Machine Learning
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A Deep-Learning Sequence-Based Method to Predict Protein Stability Changes Upon Genetic Variations.

Genes Jun 12, 2021
Several studies have linked disruptions of protein stability and its normal functions to disease. Therefore, during the last few decades, many tools have been developed to predict the free energy changes upon protein residue variations. Most of these...
Molecular Dynamics Simulation Humans Genetic Variation Amino Acid Substitution Protein Stability Deep Learning Sequence Analysis, Protein
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Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen.

Nature communications Jun 10, 2021
Species harbor extensive structural variation underpinning recent adaptive evolution. However, the causality between genomic features and the induction of new rearrangements is poorly established. Here, we analyze a global set of telomere-to-telomere...
Phylogeny Genome-Wide Association Study Genomics Machine Learning Computer Simulation Genetic Variation Polymorphism, Genetic Ascomycota Pedigree Polymorphism, Single Nucleotide Models, Genetic Evolution, Molecular Retroelements Crossing Over, Genetic Genes, Duplicate INDEL Mutation Meiosis Sequence Inversion Chromosomes Eukaryota Arabidopsis Genome
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MET Exon 14 Skipping: A Case Study for the Detection of Genetic Variants in Cancer Driver Genes by Deep Learning.

International journal of molecular sciences Apr 19, 2021
BACKGROUND: Disruption of alternative splicing (AS) is frequently observed in cancer and might represent an important signature for tumor progression and therapy. Exon skipping (ES) represents one of the most frequent AS events, and in non-small cell...
Humans Exons Neural Networks, Computer Deep Learning Genetic Variation
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Refinement of the clinical variant interpretation framework by statistical evidence and machine learning.

Med (New York, N.Y.) Mar 11, 2021
BACKGROUND: Although the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines for variant interpretation are used widely in clinical genetics, there is room for improvement of these knowledge-bas...
Amino Acids Humans Genetic Testing Machine Learning Genetic Variation United States
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Prioritizing non-coding regions based on human genomic constraint and sequence context with deep learning.

Nature communications Mar 8, 2021
Elucidating functionality in non-coding regions is a key challenge in human genomics. It has been shown that intolerance to variation of coding and proximal non-coding sequence is a strong predictor of human disease relevance. Here, we integrate into...
Sequence Analysis, DNA Whole Genome Sequencing Genetic Variation Genome, Human DNA, Intergenic Humans Deep Learning Genomics
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CADD-Splice-improving genome-wide variant effect prediction using deep learning-derived splice scores.

Genome medicine Feb 22, 2021
BACKGROUND: Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate synthesis of human proteins. Genetic variants impacting splicing underlie a substantial proportion of genetic disease, but are challenging to identify beyond...
Introns RNA Splicing Exons Deep Learning Genome-Wide Association Study Genetic Variation Base Sequence Humans
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Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response.

Frontiers in immunology Feb 18, 2021
Predictive models are becoming more and more commonplace as tools for candidate antigen discovery to meet the challenges of enabling epitope mapping of cohorts with diverse HLA properties. Here we build on the concept of using two key parameters, div...
Humans Genetic Variation Peptides Machine Learning Epitopes, T-Lymphocyte Viral Proteins Antigens, Viral CD8-Positive T-Lymphocytes HLA Antigens HIV Host-Pathogen Interactions Genome, Viral HIV Infections Proteome
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