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

Research output: Contribution to journalArticleResearchpeer-review

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, 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 R ; Pouton, Colin W. / Haplotyping the human leukocyte antigen system from single chromosomes. In: Scientific Reports. 2016 ; Vol. 6.
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title = "Haplotyping the human leukocyte antigen system from single chromosomes",
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.",
author = "Murphy, {Nicholas M} and Matthew Burton and Powell, {David R} and Rossello, {Fernando J} and Don Cooper and Abha Chopra and Hsieh, {Ming Je} and Sayer, {David C.} and Lavinia Gordon and Pertile, {Mark D.} and Tait, {Brian D} and Irving, {Helen R} and Pouton, {Colin W}",
year = "2016",
month = "7",
day = "27",
doi = "10.1038/srep30381",
language = "English",
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Murphy, NM, Burton, M, Powell, DR, Rossello, FJ, Cooper, D, Chopra, A, Hsieh, MJ, Sayer, DC, Gordon, L, Pertile, MD, Tait, BD, Irving, HR & Pouton, CW 2016, 'Haplotyping the human leukocyte antigen system from single chromosomes' Scientific Reports, vol. 6, 30381. https://doi.org/10.1038/srep30381

Haplotyping the human leukocyte antigen system from single chromosomes. / 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 R; Pouton, Colin W.

In: Scientific Reports, Vol. 6, 30381, 27.07.2016.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Murphy, Nicholas M

AU - Burton, Matthew

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AU - Rossello, Fernando J

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AU - Hsieh, Ming Je

AU - Sayer, David C.

AU - Gordon, Lavinia

AU - Pertile, Mark D.

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AU - Irving, Helen R

AU - Pouton, Colin W

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