The use of Sequence Based Typing (SBT) as a method for defining the HLA type is well documented, most SBT typing strategies currently employed use the exon 2 and exon 3 sequences for HLA class I analysis and exon 2 alone for HLA class II analysis. Due to the heterozygous nature of the SBT analysis the combinations of many pairs of alleles may give an ambiguous typing result. The document includes a list of all alleles which are identical over exons 2+3 for HLA class I and exon 2 for HLA class II, in addition all ambiguous results obtained when using the alleles included in this release are also included.
From 01 April 2010, all groups of HLA alleles that have identical nucleotide sequences across the exons encoding the peptide binding domains (exon 2 and 3 for HLA class I and exon 2 only for HLA class II alleles) are designated by an upper case ‘G’ which follows the allele designation of the lowest numbered allele in the group. A full list of these groups can be seen at http://hla.alleles.org/nomenclature/g_groups.html.
Generating Ambiguous Allele Combinations
The algorithm used to generate the G groups does include alleles which contain unsequenced regions. For the alleles in question, the sequence of an alternate allele has been used to extend the sequence over this region. Where possible a genomic or silent variant of the unsequenced allele are used, when this is not possible an alternate allele from within the same first field groupis used and only used when there is a high probability that the sequence used would be shown to be correct if the region was fully sequenced. The list of alleles containing unsequenced regions and the alternate alleles used to infer the missing sequence are detailed in the file.
In the case of unsequenced regions that cannot be accurately be inferred from known sequences with a high level of confidence the allele has been omitted from the analysis.
We recognise that future sequencing of unsequenced regions may reveal disparity between the predicted sequence and the newly sequenced region. We therefore welcome any further information which will help improve analysis of these regions.
Download Ambiguous Allele Combinations files
The IMGT/HLA Ambiguous Allele Combinations file is available as both a XML file and Microsoft Excel file for the current release. The PDF version of the file is no longer being made available from this website because the number of cominations increases rapidly with each release of new alleles. For this reason, we would encourage our users to use the XLS and XML formats where possible. We welcome feedback from our users on which of the Ambiguous Allele Combinations files are been used, to allow us to investigate the most appropriate methods for publishing this data. Please send any feedback on these files to email@example.com with the subject line "Ambigs".
Previous releases are available as PDF, XLS and XML files.
Download pre-2010 Nomenclature Files
The IMGT/HLA Ambiguous Allele Combinations file is available as both a PDF file and Microsoft Excel file.
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