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Overview

The GL String Code (GLSC) code system described here combines Genotype List String (GL String) grammar with established HLA and KIR nomenclatures, thereby specifying 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.

GL String grammar1 is a string format for genotyping results from genetic systems with defined nomenclatures, such as HLA and KIR. 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

See the following for GLSC syntax details.

GLSC 1.0 Syntax

About HLA

The HLA gene family provides instructions for making a group of related proteins known as the human leukocyte antigen (HLA) complex. The HLA complex helps the immune system distinguish the body’s own proteins from proteins made by foreign invaders such as viruses and bacteria.2

The HLA gene system plays an important role in the human body and immune system, and it’s medical and clinical significance is extensive, with known areas of impact including transplantation, drug reactions (pharmacogenomics), 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.3

Extensibility

Topic: Registration process and/or workflow for defining a new namespace.
Topic: Mechanism for using a DNS name, e.g. xyz.org as namespace?

References

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

  2. Histocompatibility complex, U.S. National Library of Medicine (archived) 

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