The database receives a large number of queries, please check to see if the answer to your question is listed below, before contacting the IPD-IMGT/HLA team.
If you can't find the answer to your question listed below, please contact IPD-IMGT/HLA Support.
- What is an HLA Allele?
- I need a donor, can you help?
- What does this typing mean?
- Is there an HGVS style description for an HLA allele?
- Do you have the dbSNP or RS ID for a particular SNP or combination for a particular allele?
- How can I change the size of the text in the alignments?
- What does the 'Q' mean?
- What is the frequency of a certain allele in the following populations?
- How should I cite the database?
- How do I report problems with a particular tool?
- I can't find the sequence of HLA-A?
- I want the sequences in this particular format?
- I am having trouble with the sequencing software from a particular company?
What is an HLA Allele?
Within the HLA field we refer to sequences as alleles. These alleles are a combination of the SNPs seen in the sequence. Each allele is a unique sequence that differs by at least 1 change from another HLA allele. This change could be a single or multiple substitutions, insertions or deletions. Each sequence is given a unique allele ID i.e. HLA00001 and a unique HLA name i.e. HLA-A*01:01:01:01
I need a donor, can you help?
The IPD-IMGT/HLA Database often receives emails from patients or members of their family, asking if we can provide or search for a donor. Unfortunately, we are not a register of unrelated bone marrow (stem cell) donors, and so cannot provide a suitably matched donor for transplants. Details of how a search for an unrelated stem cell donor is done is given on the web site of Bone Marrow Donors Worldwide (BMDW). See http://www.bmdw.org/index.php?id=for_patients
What does this typing mean?
The IPD-IMGT/HLA Database often receives emails from patients or members of their family and prospective donors, asking if we can explain typing results or an HLA profile they have received. The format of the results will vary depending on the techniques and the centre used. In general results it will list the genes tested and then for each gene the alleles (the different variants) at that gene either in a numerical string or in a coded format. Please be aware that we cannot give medical advice on any typings sent to us, our reply, where appropriate, will be restricted to explaining what part of the code represents the gene and what represents the allele variants.
Is there an HGVS style description for an HLA allele?
Yes, the allele report tool, can be used to access a HGVS style description for each allele. This can be found by viewing the allele report and the then following the ‘View HGVS Report” link. Please see our page about the use of IPD-IMGT/HLA in Genomics Analysis for further information.
Do you have the dbSNP or RS ID for a particular SNP or combination for a particular allele?
In short, no, the IPD-IMGT/HLA database acts as repository for the allele sequences, and not the SNPs, with the HLA field, when viewing the variants these are considered in line with all SNPs in a sequence to form the allele. For this reason, less emphasis is placed upon the individual SNPs and the need to catalog these. It is the combination of SNPs that we focus on and not the individual entries. Please see our page about the use of IPD-IMGT/HLA in Genomics Analysis for further information.
How can I change the size of the text in the alignments?
Depending on your browser you will need to do the following to change the size of text viewed.
- In Firefox, Mozilla and Netscape hold 'Ctrl' and press '+' or '-' to change the size of the text.
- In Internet Explorer 7 you can hold 'Ctrl' and press '+' or '-' to change the size of the text. In Internet Explorer 6 you may need to change the browser's default settings.
Please follow the instructions below to enable you to resize the text:
- Select "Tools" from the main menu or press "Alt" and "t"
- Select "Internet Options" from the "Tools" menu or press "Alt" and "o"
- Select "Accessibility" from the options screen or press "Alt" and "e"
- Check the box for "Ignore Font sizes specified in web pages" or press "Alt" and "z"
- Confirm this selection using "Ok"
- Select "View" from the main menu or press "Alt" and "v"
- Select "Text Size" from the "Tools" menu or press "x"
- Choose the new text size
- Safari users need to hold the 'Apple' key and press '+' or '-' in order to change the size of the text.
- In Opera, press '+' or '-' to change the size of the text.
What does the 'Q' mean?
A list of all suffixes used in allele names can be found here.
What is the frequency of a certain allele in the following populations?
The IPD-IMGT/HLA Database does not store allele frequency data. We recommend the following sources of data:
- The HLA FactsBook - Steven Marsh, Peter Parham, Linda Barber available from Academic Press
- describes the frequencies of alleles in different populations,
at various polymorphic regions within Histocompatibility and Immunogenetics.
Data may be searched under country,region,ethnic origin.
How should I cite the database?
For citations please use:
The IPD and IPD-IMGT/HLA Database: allele variant databasesNucleic Acids Research (2015), 43:D423-31Full Text available from Nucleic Acids Research or Download PDF File
Reports problems with a particular tool
If you are having trouble with a specific tool, the alignment tool for instance, please first see if the solution is listed in the help pages provided. If this does not solve the problem contact IPD-IMGT/HLA Support. The e-mail should list the name of the tool and all the parameters used. For instance if an alignment failed to work then you should include the values used for the Locus, Specific Sequences, Type, Reference, Display, Formatting and "Cut & Paste". This better enables us to replicate and diagnose the problem.
I can't find the sequence of HLA-A?
We often get enquiries asking for a single sequence for a locus. For example, a request for the sequence of HLA-A where there is not one single sequence which represents HLA-A, this locus currently has over three thousand alleles.
I want the sequences in this particular format?
Please check the FTP directory before asking for sequences in a particular format. The FTP directory contains copies of the database as FASTA, PIR and MSF formatted files. It also contains EMBL-like flat files and copies of the text versions of the alignments.
If you are unable to access our FTP directory we also make this data available on our Github account here: https://github.com/ANHIG/IMGTHLA.
I am having trouble with the sequencing software from a particular company?
We cannot advise or support external software. If you are experiencing software trouble when sequencing HLA alleles please contact the support line for that particular make of software.