title: ASAFE: ancestry-specific allele frequency estimation.
abstract: In a genome-wide association study (GWAS) of an admixed population, such as Hispanic Americans, ancestry-specific allele frequencies can inform the design of a replication GWAS. We derive an EM algorithm to estimate ancestry-specific allele frequencies for a bi-allelic marker given genotypes and local ancestries on a 3-way admixed population, when the phase of each admixed individual's genotype relative to the pair of local ancestries is unknown. We call our algorithm Ancestry Specific Allele Frequency Estimation (ASAFE). We demonstrate that ASAFE has low error on simulated data.
  
  
  
  The R source code for ASAFE is available for download at https://github.com/BiostatQian/ASAFE CONTACT: qszhang@uw.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Medicine Department of Biostatistics and.
authors.forename: Qian S
authors.initials: QS
authors.lastname: Zhang
authors.affiliation: Department of Biostatistics and Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
authors.forename: Brian L
authors.initials: BL
authors.lastname: Browning
authors.affiliation: Department of Biostatistics and.
authors.forename: Sharon R
authors.initials: SR
authors.lastname: Browning
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D005787:Gene Frequency; D005828:Genetics, Population / Q000379:methods*; D015894:Genome, Human; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans