Cargando…

Comparison of Genotype Imputation for SNP Array and Low-Coverage Whole-Genome Sequencing Data

Genotype imputation is the term used to describe the process of inferring unobserved genotypes in a sample of individuals. It is a key step prior to a genome-wide association study (GWAS) or genomic prediction. The imputation accuracy will directly influence the results from subsequent analyses. In...

Descripción completa

Detalles Bibliográficos
Autores principales:	Deng, Tianyu, Zhang, Pengfei, Garrick, Dorian, Gao, Huijiang, Wang, Lixian, Zhao, Fuping
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Frontiers Media S.A. 2022
Materias:	Genetics
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8762119/ https://www.ncbi.nlm.nih.gov/pubmed/35046990 http://dx.doi.org/10.3389/fgene.2021.704118

Ejemplares similares

Exploring the optimal strategy of imputation from SNP array to whole-genome sequencing data in farm animals
por: Jiang, Yifan, et al.
Publicado: (2022)

Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation
por: Flannick, Jason, et al.
Publicado: (2012)

Optimizing Selection of the Reference Population for Genotype Imputation From Array to Sequence Variants
por: Butty, Adrien M., et al.
Publicado: (2019)

Imputation of Microsatellite Alleles from Dense SNP Genotypes for Parental Verification
por: McClure, Matthew, et al.
Publicado: (2012)

Whole genome SNP genotype piecemeal imputation
por: Wang, Yining, et al.
Publicado: (2015)

Ultra Low-Coverage Whole-Genome Sequencing as an Alternative to Genotyping Arrays in Genome-Wide Association Studies
por: Chat, Vylyny, et al.
Publicado: (2022)

Genomic Prediction Based on SNP Functional Annotation Using Imputed Whole-Genome Sequence Data in Korean Hanwoo Cattle
por: Lopez, Bryan Irvine M., et al.
Publicado: (2021)

SNP imputation bias reduces effect size determination
por: Khankhanian, Pouya, et al.
Publicado: (2015)

GWAS on Imputed Whole-Genome Resequencing From Genotyping-by-Sequencing Data for Farrowing Interval of Different Parities in Pigs
por: Wu, Pingxian, et al.
Publicado: (2019)

GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data
por: Wang, Xiaoqing, et al.
Publicado: (2022)

A nested mixture model for genomic prediction using whole-genome SNP genotypes
por: Zeng, Jian, et al.
Publicado: (2018)

Imputation-Based Genomic Coverage Assessments of Current Human Genotyping Arrays
por: Nelson, Sarah C., et al.
Publicado: (2013)

Impact of pre-imputation SNP-filtering on genotype imputation results
por: Roshyara, Nab Raj, et al.
Publicado: (2014)

Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data
por: Ceballos, Francisco C., et al.
Publicado: (2018)

Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds
por: McClure, Matthew C., et al.
Publicado: (2013)

Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken
por: Ni, Guiyan, et al.
Publicado: (2015)

Strategies for Obtaining and Pruning Imputed Whole-Genome Sequence Data for Genomic Prediction
por: Ye, Shaopan, et al.
Publicado: (2019)

Japonica array: improved genotype imputation by designing a population-specific SNP array with 1070 Japanese individuals
por: Kawai, Yosuke, et al.
Publicado: (2015)

Scanning and Filling: Ultra-Dense SNP Genotyping Combining Genotyping-By-Sequencing, SNP Array and Whole-Genome Resequencing Data
por: Torkamaneh, Davoud, et al.
Publicado: (2015)

Accuracy of prediction of simulated polygenic phenotypes and their underlying quantitative trait loci genotypes using real or imputed whole-genome markers in cattle
por: Hassani, Saeed, et al.
Publicado: (2015)

Replacement of microsatellite markers by imputed medium-density SNP arrays for parentage control in German warmblood horses
por: Nolte, Wietje, et al.
Publicado: (2022)

Assessment of Imputation Quality: Comparison of Phasing and Imputation Algorithms in Real Data
por: Stahl, Katharina, et al.
Publicado: (2021)

Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping
por: Bernard, Maria, et al.
Publicado: (2022)

Reliabilities of Genomic Prediction for Young Stock Survival Traits Using 54K SNP Chip Augmented With Additional Single-Nucleotide Polymorphisms Selected From Imputed Whole-Genome Sequencing Data
por: Gebreyesus, Grum, et al.
Publicado: (2021)

A comprehensive evaluation of polygenic score and genotype imputation performances of human SNP arrays in diverse populations
por: Nguyen, Dat Thanh, et al.
Publicado: (2022)

Fast accurate missing SNP genotype local imputation
por: Wang, Yining, et al.
Publicado: (2012)

Evaluation of low-density SNP panels and imputation for cost-effective genomic selection in four aquaculture species
por: Kriaridou, Christina, et al.
Publicado: (2023)

Functional Partitioning of Genomic Variance and Genome-Wide Association Study for Carcass Traits in Korean Hanwoo Cattle Using Imputed Sequence Level SNP Data
por: Bhuiyan, Mohammad S. A., et al.
Publicado: (2018)

Design of a Bovine Low-Density SNP Array Optimized for Imputation
por: Boichard, Didier, et al.
Publicado: (2012)

Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle
por: Li, Hongwei, et al.
Publicado: (2021)

Evaluation of SNP Genotyping in Alpacas Using the Bovine HD Genotyping Beadchip
por: More, Manuel, et al.
Publicado: (2019)

Inference of Ancestries and Heterozygosity Proportion and Genotype Imputation in West African Cattle Populations
por: Gebrehiwot, Netsanet Z., et al.
Publicado: (2021)

Genome Sequencing of Blacklip and Greenlip Abalone for Development and Validation of a SNP Based Genotyping Tool
por: Kijas, James, et al.
Publicado: (2019)

A combined long-range phasing and long haplotype imputation method to impute phase for SNP genotypes
por: Hickey, John M, et al.
Publicado: (2011)

Genome-Wide Association Study of Meat Quality Traits in Hanwoo Beef Cattle Using Imputed Whole-Genome Sequence Data
por: Bedhane, Mohammed, et al.
Publicado: (2019)

Imputation to whole-genome sequence and its use in genome-wide association studies for pork colour traits in crossbred and purebred pigs
por: Heidaritabar, Marzieh, et al.
Publicado: (2022)

Deriving Gene Networks from SNP Associated with Triacylglycerol and Phospholipid Fatty Acid Fractions from Ribeyes of Angus Cattle
por: Buchanan, Justin W., et al.
Publicado: (2016)

Genotype Imputation for Latinos Using the HapMap and 1000 Genomes Project Reference Panels
por: Gao, Xiaoyi, et al.
Publicado: (2012)

Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement
por: Zhao, Fuping, et al.
Publicado: (2023)

Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle
por: Khatkar, Mehar S, et al.
Publicado: (2012)

Cannot write session to /tmp/vufind_sessions/sess_4u9m4hkffp85lehigc7blb1vdo