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

Cite this

Murphy, N. M., Burton, M., Powell, D. R., Rossello, F. J., Cooper, D., Chopra, A., Hsieh, M. J., Sayer, D. C., Gordon, L., Pertile, M. D., Tait, B. D., Irving, H. R., & Pouton, C. W. (2016). Haplotyping the human leukocyte antigen system from single chromosomes. Scientific Reports, 6, [30381]. https://doi.org/10.1038/srep30381