AIMC Topic: Polymorphism, Single Nucleotide

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Deep neural network improves the estimation of polygenic risk scores for breast cancer.

Journal of human genetics Oct 2, 2020
Polygenic risk scores (PRS) estimate the genetic risk of an individual for a complex disease based on many genetic variants across the whole genome. In this study, we compared a series of computational models for estimation of breast cancer PRS. A de...
Genetic Predisposition to Disease Polymorphism, Single Nucleotide Neural Networks, Computer Multifactorial Inheritance Algorithms Case-Control Studies Phenotype Humans Genome-Wide Association Study Breast Neoplasms ROC Curve Biomarkers, Tumor Female Risk Factors
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A genotype imputation method for de-identified haplotype reference information by using recurrent neural network.

PLoS computational biology Oct 1, 2020
Genotype imputation estimates the genotypes of unobserved variants using the genotype data of other observed variants based on a collection of haplotypes for thousands of individuals, which is known as a haplotype reference panel. In general, more ac...
Genotype Models, Genetic Neural Networks, Computer Databases, Genetic Genomics Haplotypes Polymorphism, Single Nucleotide
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The application of deep learning for the classification of correct and incorrect SNP genotypes from whole-genome DNA sequencing pipelines.

Journal of applied genetics Sep 29, 2020
A downside of next-generation sequencing technology is the high technical error rate. We built a tool, which uses array-based genotype information to classify next-generation sequencing-based SNPs into the correct and the incorrect calls. The deep le...
Whole Genome Sequencing Genotyping Techniques Algorithms Animals Deep Learning Cattle Polymorphism, Single Nucleotide
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Genome-wide association study-based deep learning for survival prediction.

Statistics in medicine Sep 24, 2020
Informative and accurate survival prediction with individualized dynamic risk profiles over time is critical for personalized disease prevention and clinical management. The massive genetic data, such as SNPs from genome-wide association studies (GWA...
Polymorphism, Single Nucleotide Machine Learning Deep Learning Genome-Wide Association Study Neural Networks, Computer
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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...
Disease Molecular Sequence Annotation Histones Models, Genetic Alleles Genome, Human Linkage Disequilibrium Humans Phenotype Genetic Predisposition to Disease Polymorphism, Single Nucleotide Deep Learning Genome-Wide Association Study
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Genomic risk scores for juvenile idiopathic arthritis and its subtypes.

Annals of the rheumatic diseases Sep 4, 2020
OBJECTIVES: Juvenile idiopathic arthritis (JIA) is an autoimmune disease and a common cause of chronic disability in children. Diagnosis of JIA is based purely on clinical symptoms, which can be variable, leading to diagnosis and treatment delays. De...
Female Risk Factors Male Adolescent Humans Machine Learning Polymorphism, Single Nucleotide Arthritis, Juvenile Cohort Studies Child Genetic Predisposition to Disease
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Assessment of and polymorphisms in age-related macular degeneration using classic and machine-learning approaches.

Ophthalmic genetics Aug 24, 2020
BACKGROUND: and are pivotal genes driving increased risk for age-related macular degeneration (AMD) among several populations. Here, we performed a hospital-based case-control study to evaluate the effects of three single nucleotide polymorphisms (...
Polymorphism, Single Nucleotide Humans Female Macular Degeneration Complement Factor H Male Machine Learning Aged Ethnicity High-Temperature Requirement A Serine Peptidase 1 Case-Control Studies Phenotype Genetic Predisposition to Disease
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Machine Learning based histology phenotyping to investigate the epidemiologic and genetic basis of adipocyte morphology and cardiometabolic traits.

PLoS computational biology Aug 14, 2020
Genetic studies have recently highlighted the importance of fat distribution, as well as overall adiposity, in the pathogenesis of obesity-associated diseases. Using a large study (n = 1,288) from 4 independent cohorts, we aimed to investigate the re...
Body Mass Index Obesity Adipose Tissue Adipocytes Neural Networks, Computer Cell Size Machine Learning Genome-Wide Association Study Adult Polymorphism, Single Nucleotide Phenotype Male Computational Biology Humans Female Middle Aged
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Artificial intelligence powered statistical genetics in biobanks.

Journal of human genetics Aug 11, 2020
Large-scale, sometimes nationwide, prospective genomic cohorts biobanking rich biological specimens such as blood, urine and tissues, have been established and released their vast amount of data in several countries. These genetic and epidemiological...
Humans Biological Specimen Banks Polymorphism, Single Nucleotide Artificial Intelligence Reproducibility of Results Genome, Human Genetic Association Studies Genome-Wide Association Study Computational Biology Genomics
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Functional fine-mapping of noncoding risk variants in amyotrophic lateral sclerosis utilizing convolutional neural network.

Scientific reports Jul 30, 2020
Recent large-scale genome-wide association studies have identified common genetic variations that may contribute to the risk of amyotrophic lateral sclerosis (ALS). However, pinpointing the risk variants in noncoding regions and underlying biological...
Chromosomes, Human, Pair 17 Chromosomes, Human, Pair 3 Genetic Predisposition to Disease Humans Polymorphism, Single Nucleotide Neural Networks, Computer Amyotrophic Lateral Sclerosis Genome-Wide Association Study
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