Haplotyping the human leukocyte antigen system from single chromosomes Academic Article uri icon


  • We describe a method for determining the parental HLA haplotypes of a single individual without recourse to conventional segregation genetics. Blood samples were cultured to identify and sort chromosome 6 by bivariate flow cytometry. Single chromosome 6 amplification products were confirmed with a single nucleotide polymorphism (SNP) array and verified by deep sequencing to enable assignment of both alleles at the HLA loci, defining the two haplotypes. This study exemplifies a rapid and efficient method of haplotyping that can be applied to any chromosome pair, or indeed all chromosome pairs, using a single sorting operation. The method represents a cost-effective approach to complete phasing of SNPs, which will facilitate a deeper understanding of the links between SNPs, gene regulation and protein function.


  • Murphy, Nicholas M
  • Burton, Matthew
  • Powell, David R
  • Rossello, Fernando J
  • Cooper, Don
  • Chopra, Abha
  • Hsieh, Ming Je
  • Sayer, David C
  • Gordon, Lavinia
  • Pertile, Mark D
  • Tait, Brian D
  • Irving, Helen
  • Pouton, Colin W

publication date

  • 2016