Generation of full-length class i human leukocyte antigen gene consensus sequences for novel allele characterization

Peter M. Clark, Jamie L. Duke, Deborah Ferriola, Valia Bravo-Egana, Tunde Vago, Aniqa Hassan, Anna Papazoglou, Dimitri Monos

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

BACKGROUND: Routine, high-resolution human leukocyte antigen (HLA) genotyping by next generation sequencing within clinical immunogenetics laboratories can now provide the full-length gene sequence characterization of fully phased HLA alleles. This powerful technique provides insights into HLA variation beyond the traditionally characterized antigen recognition domain, providing sequence annotation across the entire gene including untranslated and intronic regions and may be used to characterize novel alleles from massively parallel sequencing runs. METHODS: We evaluated the utility of the Omixon Holotype HLA assay to generate credible, fully phased fulllength gene consensus sequences for 50 individuals at major histocompatibility complex, class I, A (HLA-A), HLA-B, and HLA-C loci (300 genotyped alleles in total) to identify and characterize novel class I HLA alleles using our downstream analytical pipeline. RESULTS: Our analysis revealed that 7.7% (23/300) of genotyped class I HLA alleles contain novel polymorphisms. Interestingly, all of the novel alleles identified by our analysis were found to harbor sequence variations within intronic regions of the respective locus. In total our analysis identified 17 unique novel class I HLA alleles from 23 of the 300 genotyped alleles and generated fulllength gene sequence annotations for 9 previously incompletely annotated HLA class I allele sequences derived from 14 of the 300 genotyped alleles. CONCLUSIONS: The demonstrated utility of the Omixon Holotype HLA assay in combination with our downstream analytical framework to generate fully phased, full-length gene consensus sequences for the identification and characterization of novel HLA alleles, facilitates the study of HLA polymorphism beyond the antigen recognition domain in human health and disease.

Original languageEnglish (US)
Pages (from-to)1630-1638
Number of pages9
JournalClinical Chemistry
Volume62
Issue number12
DOIs
StatePublished - Dec 2016

Fingerprint

Consensus Sequence
HLA Antigens
Genes
Alleles
Polymorphism
Assays
Clinical laboratories
Untranslated Regions
Molecular Sequence Annotation
Antigens
High-Throughput Nucleotide Sequencing
Antigenic Variation
Immunogenetics
Ports and harbors
Major Histocompatibility Complex

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, medical

Cite this

Generation of full-length class i human leukocyte antigen gene consensus sequences for novel allele characterization. / Clark, Peter M.; Duke, Jamie L.; Ferriola, Deborah; Bravo-Egana, Valia; Vago, Tunde; Hassan, Aniqa; Papazoglou, Anna; Monos, Dimitri.

In: Clinical Chemistry, Vol. 62, No. 12, 12.2016, p. 1630-1638.

Research output: Contribution to journalArticle

Clark, Peter M. ; Duke, Jamie L. ; Ferriola, Deborah ; Bravo-Egana, Valia ; Vago, Tunde ; Hassan, Aniqa ; Papazoglou, Anna ; Monos, Dimitri. / Generation of full-length class i human leukocyte antigen gene consensus sequences for novel allele characterization. In: Clinical Chemistry. 2016 ; Vol. 62, No. 12. pp. 1630-1638.
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abstract = "BACKGROUND: Routine, high-resolution human leukocyte antigen (HLA) genotyping by next generation sequencing within clinical immunogenetics laboratories can now provide the full-length gene sequence characterization of fully phased HLA alleles. This powerful technique provides insights into HLA variation beyond the traditionally characterized antigen recognition domain, providing sequence annotation across the entire gene including untranslated and intronic regions and may be used to characterize novel alleles from massively parallel sequencing runs. METHODS: We evaluated the utility of the Omixon Holotype HLA assay to generate credible, fully phased fulllength gene consensus sequences for 50 individuals at major histocompatibility complex, class I, A (HLA-A), HLA-B, and HLA-C loci (300 genotyped alleles in total) to identify and characterize novel class I HLA alleles using our downstream analytical pipeline. RESULTS: Our analysis revealed that 7.7{\%} (23/300) of genotyped class I HLA alleles contain novel polymorphisms. Interestingly, all of the novel alleles identified by our analysis were found to harbor sequence variations within intronic regions of the respective locus. In total our analysis identified 17 unique novel class I HLA alleles from 23 of the 300 genotyped alleles and generated fulllength gene sequence annotations for 9 previously incompletely annotated HLA class I allele sequences derived from 14 of the 300 genotyped alleles. CONCLUSIONS: The demonstrated utility of the Omixon Holotype HLA assay in combination with our downstream analytical framework to generate fully phased, full-length gene consensus sequences for the identification and characterization of novel HLA alleles, facilitates the study of HLA polymorphism beyond the antigen recognition domain in human health and disease.",
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