AIMC Topic: Polymorphism, Single Nucleotide

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Deep learning-based phenotype imputation on population-scale biobank data increases genetic discoveries.

Nature genetics Nov 20, 2023
Biobanks that collect deep phenotypic and genomic data across many individuals have emerged as a key resource in human genetics. However, phenotypes in biobanks are often missing across many individuals, limiting their utility. We propose AutoComplet...
Humans Phenotype Polymorphism, Single Nucleotide Deep Learning Genotype Genome-Wide Association Study Biological Specimen Banks
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disperseNN2: a neural network for estimating dispersal distance from georeferenced polymorphism data.

BMC bioinformatics Oct 11, 2023
Spatial genetic variation is shaped in part by an organism's dispersal ability. We present a deep learning tool, disperseNN2, for estimating the mean per-generation dispersal distance from georeferenced polymorphism data. Our neural network performs ...
Humans Neural Networks, Computer Software Genome Genomics Polymorphism, Single Nucleotide
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Machine learning-based ensemble approach in prediction of lung cancer predisposition using XRCC1 gene polymorphism.

Journal of biomolecular structure & dynamics Aug 6, 2023
The employment of machine learning approaches has shown promising results in predicting cancer. In the current study, polymorphisms data of five single nucleotide polymorphisms (SNPs) of DNA repair gene XRCC1 (XRCC1 399, XRCC1 194, XRCC1 206, XRCC1 6...
Polymorphism, Single Nucleotide X-ray Repair Cross Complementing Protein 1 Humans Lung Neoplasms Genetic Predisposition to Disease Machine Learning
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deepGBLUP: joint deep learning networks and GBLUP framework for accurate genomic prediction of complex traits in Korean native cattle.

Genetics, selection, evolution : GSE Jul 31, 2023
BACKGROUND: Genomic prediction has become widespread as a valuable tool to estimate genetic merit in animal and plant breeding. Here we develop a novel genomic prediction algorithm, called deepGBLUP, which integrates deep learning networks and a geno...
Quantitative Trait Loci Multifactorial Inheritance Animals Deep Learning Cattle Genotype Models, Genetic Phenotype Genomics Bayes Theorem Republic of Korea Polymorphism, Single Nucleotide
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Detecting SNP markers discriminating horse breeds by deep learning.

Scientific reports Jul 18, 2023
The assignment of an individual to the true population of origin using a low-panel of discriminant SNP markers is one of the most important applications of genomic data for practical use. The aim of this study was to evaluate the potential of differe...
Polymorphism, Single Nucleotide Genotype Horses Plant Breeding Alleles Animals Deep Learning
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Explainable multi-task learning improves the parallel estimation of polygenic risk scores for many diseases through shared genetic basis.

PLoS computational biology Jul 7, 2023
Many complex diseases share common genetic determinants and are comorbid in a population. We hypothesized that the co-occurrences of diseases and their overlapping genetic etiology can be exploited to simultaneously improve multiple diseases' polygen...
Polymorphism, Single Nucleotide Multifactorial Inheritance Learning Humans Risk Factors Neural Networks, Computer Genetic Predisposition to Disease
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A simulative deep learning model of SNP interactions on chromosome 19 for predicting Alzheimer's disease risk and rates of disease progression.

Alzheimer's & dementia : the journal of the Alzheimer's Association Jul 6, 2023
BACKGROUND: Identifying genetic patterns that contribute to Alzheimer's disease (AD) is important not only for pre-symptomatic risk assessment but also for building personalized therapeutic strategies.
Chromosomes, Human, Pair 19 Alzheimer Disease Neuroimaging Polymorphism, Single Nucleotide Magnetic Resonance Imaging Disease Progression Deep Learning Humans
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Sampling effect in predicting the evolutionary response of populations to climate change.

Molecular ecology resources Jun 30, 2023
Genomic data and machine learning approaches have gained interest due to their potential to identify adaptive genetic variation across populations and to assess species vulnerability to climate change. By identifying gene-environment associations for...
Polymorphism, Single Nucleotide Genetic Variation Climate Change Genetics, Population
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DeepCGP: A Deep Learning Method to Compress Genome-Wide Polymorphisms for Predicting Phenotype of Rice.

IEEE/ACM transactions on computational biology and bioinformatics Jun 5, 2023
Genomic selection (GS) is expected to accelerate plant and animal breeding. During the last decade, genome-wide polymorphism data have increased, which has raised concerns about storage cost and computational time. Several individual studies have att...
Polymorphism, Single Nucleotide Genotype Deep Learning Models, Genetic Phenotype Bayes Theorem Animals Genomics Oryza
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Genomic and machine learning-based screening of aquaculture-associated introgression into at-risk wild North American Atlantic salmon (Salmo salar) populations.

Molecular ecology resources May 28, 2023
The negative genetic impacts of gene flow from domestic to wild populations can be dependent on the degree of domestication and exacerbated by the magnitude of pre-existing genetic differences between wild populations and the domestication source. Re...
Genomics Polymorphism, Single Nucleotide Aquaculture Animals Animals, Wild Microsatellite Repeats Machine Learning Genetics, Population Genetic Introgression Salmo salar North America
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