High-resolution HLA typing on large-scale sample sets over thousands of markers
The human leukocyte antigen (HLA) complex is the human version of the major histocompatibility complex (MHC); this complex includes genes responsible for immune function. Variations in these genes affect immune response, including transplant rejection as well as disease susceptibility.

The highly polymorphic nature of this region and the prevalence of pseudogenes create challenges in traditional genotyping methods. Combining the use of direct genotyping with advanced imputation methods over the extended MHC region allows accurate HLA typing from SNP genotype data.

4-digit HLA types for 11 major loci
•With Axiom HLA Analysis 1.2, you will now be able to produce accurate HLA types from any genotyping data set from Affymetrix containing high-quality genotypes of a select number of predetermined markers.

Coverage of major HLA genes
•Determine the HLA type of 11 major MHC Class I and Class II loci (see Fig. 1) with 2-digit and 4-digit resolution.
•Integrate HLA typing with genotyping data for insight into immune system variation associations with genome-wide association studies (GWAS).

Direct genotyping and imputation
•Utilize an ancestry-enriched reference panel (see Fig. 2) for populations of interest to improve accuracy of HLA typing. The current reference panel is enriched for Caucasian populations.
•Leverage allele frequency patterns and linkage disequilibrium through imputation and direct genotyping in the extended MHC region to generate accurate HLA haplotypes.
•Overcome challenges in multi-ethnic populations for high-accuracy typing of HLA loci, see the publication on Multi-Population Classical HLA Type Imputation.

Easy-to-use software
•Select and import a genotyping file in the Axiom HLA Analysis window (see Fig. 3). The software supports our array genotyping output files in .vcf format.
•Analyze HLA loci of interest: select from 11 major MHC Class I and Class II HLA loci.
•Export selected loci results for all samples in 'Full Report' for 4-digit or 2-digit resolution or for selected samples in 'Per Sample Report.'

HLA analysis of genotyping data from systems other than our genotyping arrays
Affymetrix Research Service Laboratory (ARSL) provides direct HLA analysis of any high-quality genotyping data set with sufficient coverage of markers within the extended MHC region. Please inquire for more information.

Download information and instructions
Download the latest version of the Axiom HLA Analysis 1.2 (64-bit) and install the software by following the installation instructions found in the Axiom™ HLA Analysis User Guide. This version is supported on Microsoft Windows™7 Professional (SP 1) with Quad Core Processor and can be used for analyzing data from Axiom™ Human Genotyping Solution and Genome-Wide Human SNP Array 6.0 genotyping arrays.

Please note that while any population can be analyzed with this software, lower accuracy may be observed for some loci and alleles depending on their frequency in the reference panel. The current reference panel is optimized for Caucasian populations; we are continuing to improve coverage of additional ethnicities to improve call rates and accuracy.

For a list of features and system requirements, please download the latest release notes.

Click here to download a copy of Axiom™ HLA Analysis software.
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Additional software files and analysis solutions from Affymetrix
Axiom™ Analysis Suite
Affymetrix Power Tools (APT)
Genotyping Console™ (GTC) Software
SNPolisher