HLA Description

Introduction

Human Leukocyte Antigen (HLA) are proteins expressed on the surface of white blood cells that aid the immune systems ability to fight infections from foreign entities such as Bacteria and Viruses. 

HLA is particularly important in the Transplantation of solid organs and bone marrow. When organs from an unrelated donor are transplanted into a recipient the new cells are in effect foreign and can illicit an immune response and rejection. To avoid this response HLA antigens from both the donor and recipient are matched at various HLA genes of the Human Major Histocompatibility Complex (MHC). 

This matching process or HLA typing can be done either by analyzing the genetic code of the HLA antigens (High Resolution) or by analyzing the HLA antigens themselves (Low Resolution). 

Abbott Molecular's HLA Sequencing-Based Typing (SBT) system provides the highest resolution available for the typing of HLA genes.

Software

Fast and Reliable Sequencing-based Genotyping 

In genotyping, and especially HLA genotyping, the analysis of sequence data has long been a bottleneck. The analysis is time-consuming due to software design and/or the need to manually check and edit each sequence. In HLA sequencing-based typing, this bottleneck is one of the main barriers preventing the wider uptake of this gold standard typing technique.

Conexio Genomics understands the complexity of sequencing-based genotyping. Their long experience in the field of HLA sequencing and their expertise in software development combine to provide the next generation of sequencing-based genotyping software.

The aim is to provide typing software that is easy to learn and to use, enables multiple sample analysis and provides a comprehensive quality control analysis that is critical for clinical HLA typing laboratories.

  • Easy to learn — the intuitive workflow and layout of the software makes it easy to pick up.
  • Easy to use — the process requires a minimum number of steps, there is a single analysis window and editing is made simple with the intuitive Navigator.
  • Minimal analysis time — manual intervention is minimal due to Assign SBT's unique base calling algorithm for heterozygous sequence.
  • Confidence — Assign QCTM. This built-in tool automatically assesses the quality of sequence data peak-by-peak and enables sample-by-sample and run-by-run QC analysis.
  • Flexible — the software is an open genotyping application — in addition to HLA typing, other libraries can be customized to allow other genotyping applications.


Complete and Easy to Use

  • Flexible sequencing file format
  • Analysis of multiple loci in a single project
  • Can be used for locus specific amplification protocols that result in heterozygous sequence or allele group specific protocols
  • Dynamic results tables that are updated as the sequence is edited
  • Report formats can be customized
  • HLA libraries will be updated whenever a new release is available
  • Improved analysis of heterozygous positions

Assign QC

Assign QCTM for quality analysis of sequence data is a unique approach to sequencing quality control. It enables generation of a quality analysis report for a position, a region, a sample, a locus or a sequencing run.  A novel algorithm checks sequence data for several different parameters — all of which are markers of sequence quality. For each base, a base call score (BCS) is given, the perfect quality value (QV) score is 50 (or 100 if forward and reverse bases are considered together). This score is visually present in the Assign display as boxes shaded from white to red above the electropherogram, the lighter the box the better the sequence quality (see Fig. 1). This QV score can also be applied across a whole sequence or HLA locus, for example, by averaging all the base scores to get an overall sequence quality value (see Fig. 2 and 3).


Sequence positions requiring inspection are automatically identified. Limits and cut-offs may be set to eliminate the risk associated with manual assessment of poor quality sequence data.

This allows you to rapidly and objectively measure the quality of the data — giving speedy analysis you can have confidence in.

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