Understanding HLA Nomenclature System

The human major histocompatibility complex (MHC) is a 7.6‐megabase (Mb) region on the short arm of chromosome 6 that contains more than 300 genes, approximately 20–30% of which have immune‐related function.

For a given HLA locus, the antigens encoded by the two HLA alleles are codominantly expressed, and a heterozygous individual will therefore possess two different antigens at that locus.

With the advent of DNA typing methods, it is now possible to define each class of HLA molecule by its unique sequence. The MHC was first sequenced in 1999.

Each HLA allele name has a unique number corresponding to up to four sets of digits separated by colons. The length of the allele designation is dependent on the sequence of the allele and that of its nearest relative. All alleles receive at least a four digit name.

The digits before the first colon describe the type, which often corresponds to the serological antigen carried by an allotype. The next set of digits are used to list the subtypes, numbers being assigned in the order in which DNA sequences have been determined.

ie HLA‐A*02:101:01:02N signifies an HLA‐A allele of the A2 family; it has a unique coding sequence named 101, a synonymous change named 01, and is the 02 null (N) allele. The use of colons to separate these four categories permits an unlimited number of novel alleles to be named.

In addition to the unique allele number, there are additional optional suffixes that may be added to an allele to indicate its expression status. Alleles that have been shown not to be expressed – ‘Null’ alleles – have been given the suffix ‘N’.

  • ‘L’ is used to indicate an allele which has been shown to have ‘Low’ cell surface expression when compared to normal levels.
  • ‘S’ suffix is used to denote an allele specifying a protein which is expressed as a soluble, ‘Secreted’ molecule but is not present on the cell surface.
  • ‘C’ suffix is assigned to alleles that produce proteins that are present in the ‘Cytoplasm’ and not on the cell surface.
  • ‘A’ suffix indicates an ‘Aberrant’ expression where there is some doubt as to whether a protein is actually expressed.
  • ‘Q’ suffix is used when the expression of an allele is ‘Questionable’, given that the mutation seen in the allele has been shown to affect normal expression levels in other alleles.

The image above can be simplified as below !

Clinical HLA laboratories perform various tests to support the transplant programs

  1. HLA typing of the recipient and the potential donor.
  2. Screening and identification of HLA antibodies in the recipient.
  3. Detection of antibodies in the recipient that are reactive with lymphocytes of a prospective donor (i.e., cross matching).

HLA typing can be done by

1.Serologic typing of HLA antigens: Which identifies different protein and hence can identify specificity upto 2 digit or max 4 digit in above diagram. Extent of HLA polymorphism is far higher than the number of antigen specificities.

Because of the broadly reactive nature of HLA antibodies, two or more unique sequences (e.g., HLA‐A*02:01 and *02:05) may have the same serologically defined phenotype (e.g., HLA‐A2) ie serologically indistinguishable but functionally distinct HLA allelic products.

2.Molecular typing of HLA alleles: The DNA-based typing result is consistent with a single allele as defined in a given version of the World Health Organization (WHO) HLA Nomenclature. The polymerase chain reaction (PCR)-based technology is used for clinical HLA typing as sequence-specific oligonucleotide probe (SSOP) or sequence-specific primer (SSP) or Single nucleotide based sequencing (SBT).

Note >> Serologically indistinguishable variants or subtypes of HLA class I and class II antigens were identified, and these variants are different from the wild type by a very few amino acid substitutions, but these can be functionally distinct and relevant in HLA matching for hematopoietic stem cell transplantation.

Hence >> Clinical molecular typing had to be developed in order to differentiate serologically indistinguishable but functionally distinct HLA allelic products.

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