AIMC Topic: Whole Genome Sequencing

Clear Filters Showing 41 to 50 of 71 articles

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...
Whole Genome Sequencing Genetic Variation Genome, Human DNA, Intergenic Humans Deep Learning Genomics Sequence Analysis, DNA
View on PubMed DOI

Machine Learning of Patient Characteristics to Predict Admission Outcomes in the Undiagnosed Diseases Network.

JAMA network open Feb 1, 2021
IMPORTANCE: The Undiagnosed Diseases Network (UDN) is a national network that evaluates individual patients whose signs and symptoms have been refractory to diagnosis. Providing reliable estimates of admission outcomes may assist clinical evaluators ...
Humans Machine Learning Referral and Consultation Patient Admission Rare Diseases Undiagnosed Diseases Triage Adult Area Under Curve Male Whole Genome Sequencing Middle Aged Patient Selection Female Prospective Studies Infant Adolescent Infant, Newborn Child, Preschool Computer Simulation Reproducibility of Results Child Retrospective Studies Young Adult ROC Curve
View on PubMed DOI

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...
Algorithms Whole Genome Sequencing Genotyping Techniques Animals Deep Learning Cattle Polymorphism, Single Nucleotide
View on PubMed DOI

DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework.

Computational and mathematical methods in medicine Sep 1, 2020
Although sequencing a human genome has become affordable, identifying genetic variants from whole-genome sequence data is still a hurdle for researchers without adequate computing equipment or bioinformatics support. GATK is a gold standard method fo...
Genetic Variation High-Throughput Nucleotide Sequencing Cost-Benefit Analysis Humans Genome, Human Cloud Computing Deep Learning Neural Networks, Computer Software Computational Biology Whole Genome Sequencing
View on PubMed DOI

A machine learning approach to optimizing cell-free DNA sequencing panels: with an application to prostate cancer.

BMC cancer Aug 28, 2020
BACKGROUND: Cell-free DNA's (cfDNA) use as a biomarker in cancer is challenging due to genetic heterogeneity of malignancies and rarity of tumor-derived molecules. Here we describe and demonstrate a novel machine-learning guided panel design strategy...
Base Sequence Genome, Human Circulating Tumor DNA Prostatic Neoplasms Mutation Whole Genome Sequencing Aged Aged, 80 and over Adult Biomarkers, Tumor Male Middle Aged Cohort Studies Humans Sequence Analysis, DNA Machine Learning
View on PubMed DOI

Application of Whole-Genome Sequences and Machine Learning in Source Attribution of Salmonella Typhimurium.

Risk analysis : an official publication of the Society for Risk Analysis Jun 8, 2020
Prevention of the emergence and spread of foodborne diseases is an important prerequisite for the improvement of public health. Source attribution models link sporadic human cases of a specific illness to food sources and animal reservoirs. With the ...
Disease Reservoirs Animals, Domestic Salmonella typhimurium Whole Genome Sequencing Genes, Bacterial Humans Machine Learning Algorithms Animals
View on PubMed DOI

DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure.

Genome biology Mar 26, 2020
Non-coding variants have been shown to be related to disease by alteration of 3D genome structures. We propose a deep learning method, DeepMILO, to predict the effects of variants on CTCF/cohesin-mediated insulator loops. Application of DeepMILO on v...
CCCTC-Binding Factor Chromosomal Proteins, Non-Histone Mutation Insulator Elements Humans Whole Genome Sequencing Cohesins Neoplasms Cell Cycle Proteins Deep Learning Chromatin Cell Line, Tumor
View on PubMed DOI

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.

Nature communications Feb 5, 2020
In cancer, the primary tumour's organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Can...
Male Humans Neoplasms Deep Learning Female Mutation Computational Biology Reproducibility of Results Whole Genome Sequencing Neoplasm Metastasis Genome, Human
View on PubMed DOI

VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning.

PLoS computational biology Jan 13, 2020
Antimicrobial resistance (AMR) is an increasing threat to public health. Current methods of determining AMR rely on inefficient phenotypic approaches, and there remains incomplete understanding of AMR mechanisms for many pathogen-antimicrobial combin...
Chromosome Mapping Drug Resistance, Microbial Whole Genome Sequencing Genome, Bacterial Anti-Bacterial Agents Machine Learning Bacteria Software DNA, Bacterial Algorithms Models, Statistical
View on PubMed DOI

Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data.

PLoS computational biology Sep 3, 2019
Prediction of antibiotic resistance phenotypes from whole genome sequencing data by machine learning methods has been proposed as a promising platform for the development of sequence-based diagnostics. However, there has been no systematic evaluation...
Anti-Bacterial Agents Computational Biology Humans Databases, Genetic Reproducibility of Results Genome, Bacterial Machine Learning Bacterial Infections Microbial Sensitivity Tests Algorithms Whole Genome Sequencing Bacteria
View on PubMed DOI
Popular Topics
Recent Journals