Data analysis of HLA sequencing using Assign-SBT v3.6+ from Conexio.

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.