Super High Resolution for Single Molecule-Sequence-Based Typing of Classical HLA Loci Using Ion Torrent PGM

Methods Mol Biol. 2018:1802:115-133. doi: 10.1007/978-1-4939-8546-3_8.

Abstract

Super high resolution-single molecule-sequence-based typing (SS-SBT) is an HLA DNA typing method to the field 4 level of allelic resolution (formerly known as 8-digit typing) to efficiently detect novel and null alleles without phase ambiguity by combination of long ranged PCR amplification and next-generation sequencing (NGS) technologies. In this chapter, we describe three basic steps, long ranged PCR, NGS, and allele assignment.

Keywords: Genotyping; HLA; Ion Torrent PGM; Next-generation sequencing (NGS); Super high resolution single molecule—sequence-based typing (SS-SBT); long ranged polymerase chain reaction (PCR).

MeSH terms

  • Alleles
  • Base Sequence
  • DNA / genetics
  • DNA / isolation & purification
  • Gene Library
  • Genetic Loci*
  • Genome, Human
  • HLA Antigens / genetics*
  • High-Throughput Nucleotide Sequencing / instrumentation*
  • High-Throughput Nucleotide Sequencing / methods*
  • Histocompatibility Testing / methods*
  • Humans
  • Polymerase Chain Reaction
  • Templates, Genetic

Substances

  • HLA Antigens
  • DNA