AIMC Topic: Genotyping Techniques
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SVLearn: a dual-reference machine learning approach enables accurate cross-species genotyping of structural variants.
Nature communications
Mar 11, 2025
Structural variations (SVs) are diverse forms of genetic alterations and drive a wide range of human diseases. Accurately genotyping SVs, particularly occurring at repetitive genomic regions, from short-read sequencing data remains challenging. Here,...
Development, Validation, and Implementation of an Augmented Multiwell, Multitarget Quantitative PCR for the Analysis of Human Papillomavirus Genotyping through Software Automation, Data Science, and Artificial Intelligence.
The Journal of molecular diagnostics : JMD
Jul 5, 2024
The value of human papillomavirus (HPV) testing for cervical cancer screening is well established; however, its use as a primary screening option or as a reflex test after atypical cytology results is now gaining wider acceptance. The importance of f...
Machine learning, transcriptome, and genotyping chip analyses provide insights into SNP markers identifying flower color in Platycodon grandiflorus.
Scientific reports
Apr 13, 2021
Bellflower is an edible ornamental gardening plant in Asia. For predicting the flower color in bellflower plants, a transcriptome-wide approach based on machine learning, transcriptome, and genotyping chip analyses was used to identify SNP markers. S...
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...
Machine Learning Interpretation of Extended Human Papillomavirus Genotyping by Onclarity in an Asian Cervical Cancer Screening Population.
Journal of clinical microbiology
Nov 22, 2019
This study aimed (i) to compare the performance of the BD Onclarity human papillomavirus (HPV) assay with the Cobas HPV test in identifying cervical intraepithelial neoplasia 2/3 or above (CIN2/3+) in an Asian screening population and (ii) to explore...
A machine learning approach for the identification of population-informative markers from high-throughput genotyping data: application to several pig breeds.
Animal : an international journal of animal bioscience
Oct 11, 2019
Single nucleotide polymorphisms (SNPs) able to describe population differences can be used for important applications in livestock, including breed assignment of individual animals, authentication of mono-breed products and parentage verification amo...
Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data.
Scientific reports
Jul 17, 2019
Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machin...
Genome-Wide Association Study
ROC Curve
Genetic Predisposition to Disease
Polymorphism, Single Nucleotide
Genotype
Genotyping Techniques
Logistic Models
Neural Networks, Computer
INDEL Mutation
Models, Genetic
Female
Decision Trees
Area Under Curve
Male
Deep Learning
Crohn Disease
Alleles
Humans
Nonlinear Dynamics
A multi-task convolutional deep neural network for variant calling in single molecule sequencing.
Nature communications
Mar 1, 2019
The accurate identification of DNA sequence variants is an important, but challenging task in genomics. It is particularly difficult for single molecule sequencing, which has a per-nucleotide error rate of ~5-15%. Meeting this demand, we developed Cl...
Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal .
Journal of clinical microbiology
Jan 30, 2019
Nontyphoidal species are the leading bacterial cause of foodborne disease in the United States. Whole-genome sequences and paired antimicrobial susceptibility data are available for strains because of surveillance efforts from public health agencie...
Giardia duodenalis assemblages in cats from Virginia, USA.
Veterinary parasitology, regional studies and reports
Dec 18, 2018
Giardia duodenalis is considered a species complex that is divided into 8 genetically distinct but morphologically identical assemblages (A-H). Assemblages C-H are generally host adapted, while A and B infect both people and animals and are considere...
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