Rapid genotype imputation from sequence with reference panels.
Sign Up to like & getrecommendations! Published in 2021 at "Nature genetics"
DOI: 10.1038/s41588-021-00877-0
Abstract: Inexpensive genotyping methods are essential to modern genomics. Here we present QUILT, which performs diploid genotype imputation using low-coverage whole-genome sequence data. QUILT employs Gibbs sampling to partition reads into maternal and paternal sets, facilitating… read more here.
Keywords: genotype imputation; imputation; reference panels; rapid genotype ... See more keywords
Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes
Sign Up to like & getrecommendations! Published in 2020 at "Scientific Reports"
DOI: 10.1038/s41598-020-75387-w
Abstract: Although ancient DNA data have become increasingly more important in studies about past populations, it is often not feasible or practical to obtain high coverage genomes from poorly preserved samples. While methods of accurate genotype… read more here.
Keywords: low coverage; genotype imputation; imputation; ancient genomes ... See more keywords
A fast Data-Driven method for genotype imputation, phasing, and local ancestry inference: MendelImpute.jl.
Sign Up to like & getrecommendations! Published in 2021 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btab489
Abstract: MOTIVATION Current methods for genotype imputation and phasing exploit the volume of data in haplotype reference panels and rely on hidden Markov models. Existing programs all have essentially the same imputation accuracy, are computationally intensive,… read more here.
Keywords: genotype imputation; imputation phasing; mendelimpute; method genotype ... See more keywords
Impact of the inaccessible genome on genotype imputation and genome-wide association studies
Sign Up to like & getrecommendations! Published in 2024 at "Human Molecular Genetics"
DOI: 10.1093/hmg/ddae062
Abstract: Abstract Genotype imputation is widely used in genome-wide association studies (GWAS). However, both the genotyping chips and imputation reference panels are dependent on next-generation sequencing (NGS). Due to the nature of NGS, some regions of… read more here.
Keywords: genotype imputation; genome wide; inaccessible regions; wide association ... See more keywords
Plant-ImputeDB: an integrated multiple plant reference panel database for genotype imputation
Sign Up to like & getrecommendations! Published in 2021 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkaa953
Abstract: Abstract Genotype imputation is a process that estimates missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs), boost the power… read more here.
Keywords: reference; plant imputedb; genotype imputation; plant ... See more keywords
Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation
Sign Up to like & getrecommendations! Published in 2020 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkz854
Abstract: Abstract Animal-ImputeDB (http://gong_lab.hzau.edu.cn/Animal_ImputeDB/) is a public database with genomic reference panels of 13 animal species for online genotype imputation, genetic variant search, and free download. Genotype imputation is a process of estimating missing genotypes in… read more here.
Keywords: reference panels; animal imputedb; imputation; genotype imputation ... See more keywords
Accuracy of genotype imputation in Labrador Retrievers
Sign Up to like & getrecommendations! Published in 2018 at "Animal Genetics"
DOI: 10.1111/age.12677
Abstract: Summary The dog is a valuable model species for the genetic analysis of complex traits, and the use of genotype imputation in dogs will be an important tool for future studies. It is of particular… read more here.
Keywords: genotype imputation; imputation; accuracy genotype; imputation labrador ... See more keywords
Improving the resolution of canine genome-wide association studies using genotype imputation: A study of two breeds
Sign Up to like & getrecommendations! Published in 2021 at "Animal genetics"
DOI: 10.1111/age.13117
Abstract: Summary Genotype imputation using a reference panel that combines high-density array data and publicly available whole genome sequence consortium variant data is potentially a cost-effective method to increase the density of extant lower-density array datasets.… read more here.
Keywords: array; genotype imputation; imputation; canine ... See more keywords
Novel methods for genotype imputation to whole-genome sequence and a simple linear model to predict imputation accuracy
Sign Up to like & getrecommendations! Published in 2017 at "BMC Genetics"
DOI: 10.1186/s12863-017-0588-1
Abstract: BackgroundAccurate imputation plays a major role in genomic studies of livestock industries, where the number of genotyped or sequenced animals is limited by costs. This study explored methods to create an ideal reference population for… read more here.
Keywords: genotype imputation; imputation; imputation accuracy; accuracy ... See more keywords
A genotype imputation method for de-identified haplotype reference information by using recurrent neural network
Sign Up to like & getrecommendations! Published in 2020 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1008207
Abstract: 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… read more here.
Keywords: reference panel; information; imputation; genotype imputation ... See more keywords
Genotype imputation and polygenic score estimation in northwestern Russian population
Sign Up to like & getrecommendations! Published in 2022 at "PLoS ONE"
DOI: 10.1371/journal.pone.0269434
Abstract: Numerous studies demonstrated the lack of transferability of polygenic score (PGS) models across populations and the problem arising from unequal presentation of ancestries across genetic studies. However, even within European ancestry there are ethnic groups… read more here.
Keywords: polygenic score; imputation; genotype imputation; imputation polygenic ... See more keywords