How to Search for Variants in a 4-Field HLA Typing Report Against the IMGT Database
The International ImMunoGeneTics Information System (IMGT) is a high-quality, integrated database that provides comprehensive information on immunoglobulins (IG), T cell receptors (TR), and major histocompatibility complex (MHC) molecules. In this guide, we will outline the steps to search for specific variants a researcher finds in their 4-field HLA typing report against the IMGT database.
- Preparation: First, prepare your 4-field HLA typing report. The report should contain HLA alleles, which are represented by four fields: allele group, specific protein, synonymous substitutions, and non-coding variants. An example of a 4-field HLA allele is HLA-A*02:01:01:01.
- Access the IMGT/HLA Database: Navigate to the IMGT/HLA Database website: http://www.ebi.ac.uk/ipd/imgt/hla/. This is the official site to search for HLA variants and alleles.
- Navigate to the “Allele Query” Section: On the main page, click on the “Allele Query” tab located in the top menu. This will redirect you to a page where you can search for specific HLA alleles.
- Input the HLA Allele: Enter the specific HLA allele from your 4-field HLA typing report into the search box under “Allele Name.” Ensure that you input the allele in the correct format, as shown in the example: HLA-A*02:01:01:01.
- Select the Appropriate Output Format: Choose your desired output format from the “Output Format” dropdown menu. The available formats are:
- Simple – Basic information on the HLA allele.
- Alignment – Nucleotide sequence alignment of the HLA allele.
- FASTA – Nucleotide and protein sequences in FASTA format.
- Summary – Detailed information on the HLA allele, including nucleotide and protein sequences, exon/intron organization, and references.
- Perform the Search: Click on the “Search” button to perform the query. The IMGT/HLA Database will display the results corresponding to the entered HLA allele in the chosen output format.
- Analyze the Results: Examine the search results and compare them with the information in your 4-field HLA typing report. The IMGT/HLA Database provides comprehensive information on the HLA allele, including sequence data, related alleles, and references to relevant publications.
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