Haplotyping the human leukocyte antigen system from single chromosomes

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

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Abstract

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.

Original languageEnglish
Article number30381
Number of pages9
JournalScientific Reports
Volume6
DOIs
Publication statusPublished - 27 Jul 2016

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