Overview

The Genotype List String Code (GLSC) code system1 combines Genotype List String (GL String) grammar2,3 with established HLA4 and KIR5 nomenclatures, defining a syntax for encoding of nomenclature-level genotyping results.

The established HLA and KIR nomenclatures are primarily concerned with identification and characterization of individual alleles, and do not incorporate a grammar for genotyping results.

When combined with a formal nomenclature for a genetic system, such as those for HLA and KIR, GL String grammar is able to describe genotyping results. In addition to genotyping results, the grammar can also describe data analysis artifacts such as multi-locus (multi-gene) haplotypes.

From a terminology standpoint, the result of adding a compositional grammar to an established code system such as HLA or KIR nomenclature is a new code system, because the grammar may be used to construct expressions not explicitly defined in the original system as concept codes.

In addition to its usage with HLA and KIR nomenclatures, future versions of the GLSC code system could potentially extend it for use with additional genetic nomenclature systems.

Syntax

GLSC syntax was originally defined using the GL String (2013) grammar, and later revised to use the updated GL String (2023) grammar. See the following for GLSC syntax details.

About HLA

The human leukocyte antigen (HLA) gene family is part of the major histocompatibility complex (MHC), and contributes to the ability of the immune system to respond to the multitude of different and rapidly evolving pathogens.6 It plays an important role in the human body and immune system, with known areas of impact including transplantation, drug reactions, and disease associations.

About KIR

Killer cell immunoglobulin-like receptors (KIRs) interact with natural killer (NK) cells and are likely to play a significant role in the control of the immune response. Some KIR isotypes interact with HLA molecules to inhibit NK cell activity, and other KIR isotypes stimulate NK cell activity.7

References

  1. The genotype list string code syntax for exchanging nomenclature-level genotyping results in clinical and research data management and analysis systems, Mack, et al. ↩

  2. Genotype List String: a grammar for describing HLA and KIR genotyping results in a text string, Milius, et al. ↩

  3. Genotype List String 1.1: Extending the Genotype List String grammar for describing HLA and Killer-cell Immunoglobulin-like Receptor genotypes, Mack, et al. ↩

  4. The IPD-IMGT/HLA Database, European Bioinformatics Institute (EMBL-EBI) ↩

  5. The IPD-KIR Database, European Bioinformatics Institute (EMBL-EBI) ↩

  6. Immunobiology: The Immune System in Health and Disease, Janeway, et al. ↩

  7. The KIR Gene Cluster, by Mary Carrington and Paul Norman ↩