We type Human Leucocyte Antigen (HLA) by either Illumina or Sanger DNA sequencing and we require 50µl of 50 ng/µ l of high quality (A260/A280>=1.7) to perform the full test which involves a proprietary set of 12 PCR reactions covering the major variable exons of the loci we type. Please note if other typings are required e.g. for ERAP or KIR additional material will be required
We are also able to type a subset of the MAFA LA's (Crab Eating Macaque). Please enquire
DRB1 Assignments: Reporting
The gene DRB1 is expressed at a level five times higher than its paralogues DRB3, DRB4 and DRB5. DRB1 is present in all individuals. Allelic variants of DRB1 may be linked with DRB3, DRB4 and DRB5. ‘Calls’ in the DRB1 DRB3 DRB4 and DRB5 columns can be confusing. For some DRB1 alleles different combinations of 3, 4, 5, are expected. When the assignments in 3, 4, 5 are not detected the notation NP (Not Present) is used. Occasionally a 3, 4, or 5 is expected but not detected, this is still reported as NP but a comment is generally provided (usually as a superscript indicator) denoting expected but not found
G groups are used for Reporting of Ambiguous Allele Typing (IMGT Ambiguous Alleles http://www.ebi.ac.uk/ipd/imgt/hla/ambig.html).
HLA alleles that have identical nucleotide sequences across the exons encode the peptide binding domains (exon 2 and 3 for HLA class I and exon 2 only for HLA class II alleles). They are designated by an upper case ‘G' which follows the first 3 fields of the allele designation of the lowest numbered allele in the group.
However, when typing HLA-DQB1 we can-not use the HLA-DQB G groups since we sequence exon 2 and exon 3. Although we are also sequencing exon 3, there is still ambiguity. We have chosen to make up our own groups, because allele pairs that include two sets of reads that lead to ambiguous calls can result in a large set of possible combinations. We have found when checking through these lists that involve ambiguity that it is difficult.
Hence we define iGroups as:
HLA-DQB1 alleles that have identical nucleotide sequences across the portions of exon 2 and exon 3 that are sequenced for typing, or that are identical across the portion of exon 2 that is sequenced where one or both alleles does not have reference data in the IMGT database for exon 3. Alleles in the same group will be designated by a lower case ‘i’ which follows the first 3 fields of the allele designation of the lowest numbered allele in the group.
As an example a reported iGroup of HLA-DQB1*05:03:01i encompasses all possible allele combinations of HLA-DQB1*05:03:01:01 HLA-DQB1*05:03:01:02 HLA-DQB1*05:10 as defined in the document below
HLA-DRB exon 2 sequences are partially truncated at the 5' end and therefor lead to ambiguous alleles that can result in a large set of possible combinations which makes DRB1/3/4/5 associations difficult to interpret. Hence, iGroups are used.