A method for the allocation of sequencing resources in genotyped livestock populations

Genetics, Selection, Evolution : GSE
Serap GonenJohn M Hickey

Abstract

This paper describes a method, called AlphaSeqOpt, for the allocation of sequencing resources in livestock populations with existing phased genomic data to maximise the ability to phase and impute sequenced haplotypes into the whole population. We present two algorithms. The first selects focal individuals that collectively represent the maximum possible portion of the haplotype diversity in the population. The second allocates a fixed sequencing budget among the families of focal individuals to enable phasing of their haplotypes at the sequence level. We tested the performance of the two algorithms in simulated pedigrees. For each pedigree, we evaluated the proportion of population haplotypes that are carried by the focal individuals and compared our results to a variant of the widely-used key ancestors approach and to two haplotype-based approaches. We calculated the expected phasing accuracy of the haplotypes of a focal individual at the sequence level given the proportion of the fixed sequencing budget allocated to its family. AlphaSeqOpt maximises the ability to capture and phase the most frequent haplotypes in a population in three ways. First, it selects focal individuals that collectively represent a larger portion of t...Continue Reading

References

Nov 26, 2008·Genome Research·Gary K ChenJeffrey D Wall
Apr 28, 2009·BMC Genetics·Rafael Villa-AnguloJohn J Grefenstette
Mar 11, 2011·Genetics, Selection, Evolution : GSE·John M HickeyJulius H J van der Werf
Feb 12, 2013·Journal of Medical Genetics·Luis R LopesPerry M Elliott
Apr 27, 2013·Genetics, Selection, Evolution : GSE·John M Hickey, Andreas Kranis
Oct 1, 2013·Journal of Animal Breeding and Genetics = Zeitschrift Für Tierzüchtung Und Züchtungsbiologie·J M Hickey
Jan 16, 2014·European Journal of Human Genetics : EJHG·Jane KayeUNKNOWN UK 10K
Jul 16, 2014·Genetics, Selection, Evolution : GSE·Rianne van BinsbergenRoel F Veerkamp
Mar 26, 2015·Nature Genetics·Daniel F GudbjartssonKari Stefansson
Apr 19, 2015·Genetics, Selection, Evolution : GSE·Gregor GorjancJohn M Hickey

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Citations

Oct 27, 2017·Genetics, Selection, Evolution : GSE·Roger Ros-FreixedesJohn M Hickey
Apr 7, 2020·Genetics, Selection, Evolution : GSE·Roger Ros-FreixedesJohn M Hickey
Apr 7, 2020·Genetics, Selection, Evolution : GSE·Roger Ros-FreixedesJohn M Hickey
Dec 14, 2018·Genetics, Selection, Evolution : GSE·Roger Ros-FreixedesJohn M Hickey
Dec 24, 2018·Genetics, Selection, Evolution : GSE·Martin JohnssonJohn M Hickey
May 25, 2021·Frontiers in Genetics·Deniz AkdemirJulio Isidro Y Sánchez

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Software Mentioned

AlphaSim
AlphaSeqOpt
AlphaImpute
AlphaPhase
AlphaFamSeq
Gusev
PEDIG

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