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HLA typing using next generation sequencing: An overview

from Human Immunology

The introduction of PCR based amplification [1,2] and sequencing of HLA class I and class II genes revealed a level of polymorphism far beyond the resolution of serologic or cellular based HLA typing. Now, decades later, the HLA community is still struggling to deal with this extensive and ever-expanding allelic diversity (12,542 HLA alleles as of January, 2015). The patchwork pattern of polymorphism identified by these initial sequencing studies was primarily localized to the exons that encoded the peptide binding domains of class I and class II molecules. Consequently, the analysis of HLA polymorphism based on probe hybridization (sequence specific oligonucleotide probes; SSOP) as well as on sequence-specific PCR priming (SSP) followed by amplicon detection (e.g. gel electrophoresis or fluorescence monitoring) focused on specific polymorphic sequence motifs in targeted amplicons.
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