AlphaSeqOpt: optimal allocation of fixed sequencing budget to focal individuals

John Hickey (Developer)

Research output: Non-textual formSoftware

Abstract

AlphaSeqOpt aims to optimally allocate a fixed sequencing budget to focal individuals and their families such that the final haplotypes, when phased at the sequence level, represent the maximum possible portion of the haplotype diversity in the population that can be sequenced and phased at that budget.

AlphaSeqOpt implements 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 amongst the families of the focal individuals to enable phasing of their haplotypes at the sequence level.

AlphaSeqOpt maximises the ability to capture and phase the most frequent haplotypes in a population in three ways. First, AlphaSeqOpt selects focal individuals that collectively represent a higher portion of the population haplotype diversity than standard methods. Second, AlphaSeqOpt selects focal individuals from across the pedigree whose haplotypes can be easily phased whereas standard methods mainly selects individuals from the oldest generations of the pedigree whose haplotypes would be difficult to phase and impute into distant descendants. Third, AlphaSeqOpt allocates more of the fixed sequencing budget to focal individuals whose haplotypes appear more frequently in the rest of the population than to focal individuals whose haplotypes appear less frequently. Unlike standard methods, AlphaSeqOpt allocates part of the sequencing budget to relatives of the focal individuals to ensure that their haplotypes can be phased at the sequence level. Phasing haplotypes at the sequence level is essential for subsequent imputation.

A manuscript describing AlphaSeqOpt has been submitted for publication. We are continuing to develop AlphaSeqOpt, especially for strategies that use low and ultra low coverage sequencing approaches.
Original languageEnglish
Publication statusPublished - 1 Oct 2016

Keywords

  • AlphaSeqOpt
  • sequencing
  • algorithm
  • frequent haplotypes

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