Author

Alan J. Mileham

Genus (United States)

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 2 Bioinformatics· 1 Genetics· 1

Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 3 Research Focus:benchmarking· 2 Research Focus:imputation· 2 Approach:simulation· 2 Approach:statistical model· 2 Research Focus:variant calling· 2 Organism:plant (other)· 1

Frequent Co-Authors

Gregor GorjanciD· 4 shared John M. HickeyiD· 4 shared Roger Ros‐FreixedesiD· 4 shared Andrew WhaleniD· 2 shared Mara BattaginiD· 2 shared William O Herring· 2 shared Bruce WhitelawiD· 1 shared Ching-Yi CheniD· 1 shared

Activity by Year

2018-2020 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 34 mutual co-author links

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4 shared papersGenomics

Gregor GorjancORCID

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4 papers

Recent·Most cited

Evaluation of sequencing strategies for whole-genome imputation with hybrid peeling

Roger Ros‐Freixedes, Andrew Whalen, Gregor Gorjanc, Alan J. Mileham, John M. Hickey

This study evaluates sequencing strategies for whole-genome imputation using hybrid peeling, finding that 2% of the population sequenced at 2x coverage provides high accuracy.

Genetics Selection Evolution · Apr 6, 2020Peer-reviewedGenomics

Accuracy of whole-genome sequence imputation using hybrid peeling in large pedigreed livestock populations

Roger Ros‐Freixedes, Andrew Whalen, Ching-Yi Chen, Gregor Gorjanc, William O Herring, Alan J. Mileham, John M. Hickey

This study demonstrates high accuracy of whole-genome sequence imputation in large livestock populations using hybrid peeling, with median individual-wise correlation of 0.97.

Genetics Selection Evolution · Apr 6, 2020Peer-reviewedGenomics

A strategy to exploit surrogate sire technology in livestock breeding programs

P. Gottardo, Gregor Gorjanc, Mara Battagin, R. Chris Gaynor, Janez Jenko, Roger Ros‐Freixedes, Bruce Whitelaw, Alan J. Mileham, William O Herring, John M. Hickey

This study simulates strategies for using surrogate sire technology to enhance genetic merit in livestock breeding, finding a three-stage approach most effective for maximizing genetic gain.

G3 Genes Genomes Genetics · Dec 18, 2018Peer-reviewedGenetics

Impact of index hopping and bias towards the reference allele on accuracy of genotype calls from low-coverage sequencing

Roger Ros‐Freixedes, Mara Battagin, Martin Johnsson, Gregor Gorjanc, Alan J. Mileham, Steve Rounsley, John M. Hickey

The paper shows that index hopping and reference allele bias have minimal impact on genotype calls from low-coverage sequencing, but pruning low-support haplotypes introduces a significant reference allele bias.

Genetics Selection Evolution · Dec 1, 2018Peer-reviewedBioinformatics