Advertisement

Data Analysis of HLA Sequencing Using Assign-SBT v3.6+ from Conexio

  • Carla Wirtz
  • David Sayer
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 882)

Abstract

DNA Sequencing is now a standard frontline high-throughput HLA typing procedure with some unrelated bone marrow donor registry typing laboratories performing tens of thousands of tests per year. The advantage of DNA sequencing is that, by definition, sequencing directly identifies all bases in the DNA template. Alternative molecular-based assays such as the use of sequence-specific PCR primers (PCR-SSP) and oligonucleotide probes (PCR-SSO) provide information only for those regions to which the oligos are designed and no information is obtained for the regions between primers and probes.

The era of routine high-throughput sequencing-based typing (SBT) was made possible by the development of locus-specific PCR-based assays and the development of the HLA sequencing-based typing software, Assign-SBT v3.2.7 by Conexio Genomics. A single PCR per locus simplified the template preparation stage of the test and Assign-SBT simplified the sequence analysis and allele assignment stage. Together these developments dramatically simplified the SBT procedure, making SBT cost effective.

This chapter provides a comprehensive description of Assign-SBT sequence analysis software for use in a HLA typing laboratory.

Key words

High throughput DNA sequencing Sequence analysis Assign-SBT HLA 

References

  1. 1.
    Cano P, Klitz W, Mack SJ et al (2007) Common and well-documented HLA alleles: report of the Ad-Hoc committee of the American society for histocompatibility and immunogenetics. Hum Immunol 68(5):392–417PubMedCrossRefGoogle Scholar
  2. 2.
    Bentley G, Higuchi R, Hoglund B et al (2009) High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens 74(5):393–403PubMedCrossRefGoogle Scholar
  3. 3.
    Lind C, Ferriola D, Mackiewicz K et al (2010) Next-generation sequencing: the solution for high resolution, unambiguous human leukocyte antigen typing. Hum Immunol 71(10):1033–1042PubMedCrossRefGoogle Scholar
  4. 4.
    Holcomb CL, Höglund B, Anderson MW et al (2011) A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens 77(3):206–217PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Technical Support and Training, Conexio GenomicsLongmontUSA
  2. 2.Conexio Pty LtdFremantleAustralia

Personalised recommendations