A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals.

By Brian L. Browning, Sharon R. Browning. American Journal of Human Genetics, 2009

1,682 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/2c9a9c4c96b13938639a14304e300854b2457c1b

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In Genetics

Citations in the corpus

Imputing Amino Acid Polymorphisms in Human Leukocyte Antigens (2013, methodology): “Beagle should be obtained separately from the web site http://faculty.washington.edu/ browning/beagle/beagle.html.”
Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels. (2012, methodology): “Imputation of the 50K data set to 800K genotypes was performed with BEAGLE software (Browning and Browning, 2009). Prior to this step, cross-validation was used to assess the accuracy of imputation that could be achieved. The Holstein heifers that were genotyped for the 800K panel were split into 2 ”
Designing dairy cattle breeding schemes under genomic selection: a review of international research (2012, background): “…would be to genotype a subset of animals with a high-density (e.g. 800k) SNP panel and impute SNPs to the rest of the population genotyped with lower-density SNP panels (e.g. Browning and Browning 2009; Druet and Georges 2010; Daetwyler et al. 2011; Hickey et al. 2011; VanRaden et al. 2011).”
Seven New Loci Associated with Age-Related Macular Degeneration (2013, background): “-Erich Wichmann [110,111,112,113], Thomas W Winkler [114], Tien Y Wong [24,34,35], Alan F Wright [115], Diana Zelenika [116], Li Zhang [56,64,117], Ling Zhao [56,64], Kang Zhang [56,64,117], Michael L Klein [26], Gregory S Hageman [88,118], G Mark Lathrop [71,116], Kari Stefansson [8,102], Rando All”
A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies (2009, methodology): “) The BEAGLE imputation model [12,13] is one notable exception to this point, and we discuss its alternative modeling strategy in detail in this work.”
Genotype Imputation with Millions of Reference Samples. (2016, background): “Increasing the size of reference panels is desirable because the use of larger reference panels increases imputation accuracy, particularly for lower-frequency variants.(11,12) Increasing the sequencing depth in reference”
A new approach for efficient genotype imputation using information from relatives (2014, methodology): “Allelic r2, the squared correlation between imputed genotypes and true genotypes [12], was used as a measure of imputation accuracy.”
1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana (2016, background): “In addition to groups of nearly identical individuals, 47%of North American pairs exhibit extensive haplotype sharing (total identity-by-descent length over 85 Mb, as inferred using Beagle and GERMLINE, Figure S1) (Browning and Browning, 2009; Gusev et al., 2009), indicating recent mixing among a li”
A one penny imputed genome from next generation reference panels (2018, background): “5k – 10M) and target sample sizes (10-1000) considered.”
Fast and accurate long-range phasing in a UK Biobank cohort (2015, positive): “This benchmarking procedure is commonly used to assess the accuracy of phasing and imputation pipelines [5, 9].”
Five amino acids in three HLA proteins explain most of the association between MHC and seropositive rheumatoid arthritis (2012, methodology): “We encoded all variants in the reference panel as biallelic markers, which facilitated the application of BEAGLE for imputation (using default parameters”
Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data (2013, methodology): “The HMM for haplotype frequencies determines a HMM for unrelated individuals and a HMM for parent-offspring pairs (BROWNING and BROWNING 2009).”