The developers of the IPD-IMGT/HLA Database periodically review the outputs we produce to ensure they are still relevant to and needed by our users. With the recent developments in sequencing technologies, we are currently assessing whether to stop producing files for SBT analysis in particular the files of ambiguous combinations. We would therefore request that if you are using these resources, either the Excel files, the hla_ambigs.xml file or using the online query tools, that you please contact IPD Support, with details of you name, institute and how you are using these files, so we can understand if there is a need for these files, or particular sets of data moving forward.
The use of Sequence Based Typing (SBT) as a method for defining the HLA type is well documented and most SBT typing strategies currently employed use the exon 2 and exon 3 sequences for HLA class I analysis and exon 2 for HLA class II analysis. Due to the heterozygous nature of SBT analysis, the combinations of many pairs of alleles may give an ambiguous typing result. The documents here include a list of all alleles that are identical over exons 2+3 for HLA class I and all alleles that are identical over only 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 alleles and exon 2 only for HLA class II alleles) are designated by an upper case ‘G’ which followed by the allele designation of the lowest numbered allele in the group. A full list of these groups can be viewed here.
Generating Ambiguous Allele Combinations
The algorithm used to generate the G groups does include alleles which contain unsequenced regions. For these alleles with unsequenced regions, the sequence of the most closely related allele has been used to extend the sequence over this region. Where possible, a genomic or silent variant of the unsequenced allele are used but if this is not possible then an alternate allele from within the same first field group is used - the allele is chosen based on the highest 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.
Where unsequenced regions cannot 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 currently unsequenced regions may reveal disparity between the predicted sequence and the newly sequenced region. We therefore welcome any information which will help improve analysis of these regions. Please see here for contact information.
Ambiguous Allele Combinations Search Tool
It is becoming increasingly difficult to provide a single Microsoft Excel files which covers the data required. The number of rows per worksheet can exceed 65,000 which causes issues with older versions of the software. This search tool provides an alternative method of viewing the ambiguous combinations currently detailed in the Microsoft XLS file. We welcome feedback from our users on regarding which of the Ambiguous Allele Combinations files are being used to allow us to establish the most appropriate formats for publishing this data. Please see here for information on how to get in touch.
Download Ambiguous Allele Combinations files
The IPD-IMGT/HLA Ambiguous Allele Combinations files are available in XML and Microsoft Excel formats for the current release. The PDF versions of the files are no longer being made available from this website because the number of combinations increases rapidly with the release of novel alleles. For this reason, we would encourage our users to use the XML and Microsoft Excel formats where possible. Please note that Microsoft Office 2010 or later is required to view the files.
Older releases are also available in PDF format, as well as XML and Microsoft Excel.