AIMC Topic: Genetic Variation

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Machine learning random forest for predicting oncosomatic variant NGS analysis.

Scientific reports Nov 8, 2021
Since 2017, we have used IonTorrent NGS platform in our hospital to diagnose and treat cancer. Analyzing variants at each run requires considerable time, and we are still struggling with some variants that appear correct on the metrics at first, but ...
Neural Networks, Computer Machine Learning Algorithms Biomarkers, Tumor Neoplasms Humans INDEL Mutation Oncogenes Deep Learning ROC Curve Polymorphism, Single Nucleotide Computational Biology Databases, Genetic Models, Statistical Genetic Variation High-Throughput Nucleotide Sequencing
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The viral expression and immune status in human cancers and insights into novel biomarkers of immunotherapy.

BMC cancer Nov 5, 2021
BACKGROUND: Viral infections are prevalent in human cancers and they have great diagnostic and theranostic values in clinical practice. Recently, their potential of shaping the tumor immune microenvironment (TIME) has been related to the immunotherap...
Head and Neck Neoplasms Support Vector Machine DNA, Viral Epstein-Barr Virus Infections Herpesvirus 4, Human Kaplan-Meier Estimate Genome, Viral Mutation Humans RNA-Seq Papillomaviridae Biomarkers, Tumor Tumor Virus Infections Stomach Neoplasms Machine Learning Leukocytes Immunotherapy Oncogenic Viruses Neoplasms Genetic Variation Papillomavirus Infections Tumor Microenvironment Transcriptome High-Throughput Nucleotide Sequencing Squamous Cell Carcinoma of Head and Neck
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Disease variant prediction with deep generative models of evolutionary data.

Nature Oct 27, 2021
Quantifying the pathogenicity of protein variants in human disease-related genes would have a marked effect on clinical decisions, yet the overwhelming majority (over 98%) of these variants still have unknown consequences. In principle, computational...
Genetic Fitness Evolution, Molecular Proteins Unsupervised Machine Learning Models, Molecular Genetic Variation Disease Selection, Genetic Bayes Theorem Biological Assay Humans Phenotype Genetic Predisposition to Disease
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Revisiting the out of Africa event with a deep-learning approach.

American journal of human genetics Oct 8, 2021
Anatomically modern humans evolved around 300 thousand years ago in Africa. They started to appear in the fossil record outside of Africa as early as 100 thousand years ago, although other hominins existed throughout Eurasia much earlier. Recently, s...
Deep Learning Evolution, Molecular Bayes Theorem Whole Genome Sequencing Humans Algorithms Africa Genetic Variation Monte Carlo Method Fossils
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Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships.

Nature communications Sep 24, 2021
Inferring phenotypic outcomes from genomic features is both a promise and challenge for systems biology. Using gene expression data to predict phenotypic outcomes, and functionally validating the genes with predictive powers are two challenges we add...
Arabidopsis Genetic Variation Species Specificity Genome, Plant Machine Learning Evolution, Molecular Genotype Gene Expression Regulation, Plant Phenotype Zea mays Models, Genetic Transcriptome Nitrogen Genomics
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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...
Humans Machine Learning Genetic Variation Precision Medicine Polymorphism, Single Nucleotide
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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 Gene Frequency Mutation, Missense Genome Oxidoreductases Acting on Sulfur Group Donors Brain Infant, Newborn Databases, Genetic 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 Genes, Bacterial Bacterial Outer Membrane Proteins Antigens, Bacterial Machine Learning Humans Genome, Bacterial Bacterial Proteins Streptococcal Infections Algorithms Alleles Genetic Variation Carrier Proteins Streptococcus pyogenes Evolution, Molecular
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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...
Protein Stability Amino Acid Substitution Humans Sequence Analysis, Protein Deep Learning Molecular Dynamics Simulation Genetic Variation
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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...
Genes, Duplicate Sequence Inversion Machine Learning Chromosomes Computer Simulation Evolution, Molecular Arabidopsis Genome-Wide Association Study Phylogeny Genetic Variation Genomics Retroelements Meiosis Polymorphism, Genetic Polymorphism, Single Nucleotide Crossing Over, Genetic Eukaryota Models, Genetic Ascomycota Genome Pedigree INDEL Mutation
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