GLSC 1.1 Syntax

Version 1.1

The Genotype List String Code (GLSC) code system defines a syntax for using the Genotype List String (GL String) grammar in association with a gene family namespace.

GLSC 1.1 uses a new version of the Genotype List String grammar which adds the “?” operator for ambiguous gene locations. Otherwise, GLSC 1.1 is identical to GLSC 1.0.

GL String Code Syntax

The GL String Code is composed of three required fields in a string separated by a “#” character. These fields, in order, are:

Gene family namespace
Version of the nomenclature, or the date when the GL String was created
GL String

namespace#version_or_date#glstring

See below for examples.

Gene family namespace

Each gene family namespace represents one or more code systems. When more than one code system is used, a base system is designated which is then extended by the other code systems.

For example, the hla namespace supports the IPD-IMGT/HLA allele database as the base system, as well as the National Marrow Donor Program (NMDP) multiple allele code system used to describe allele ambiguity, and the World Marrow Donor Association (WMDA) extensions (“NNNN”, “XXXX”, “UUUU” and “NEW”).

Supported namespaces

Namespace	Code System	Ref	Version Notes
`hla`	IPD-IMGT/HLA	a	tied to IPD-IMGT/HLA release version
	NMDP multiple allele code (MAC) designation	b	versionless, but usage may be tied to IPD-IMGT/HLA release version
	WMDA additional codes	c	versionless, but usage may be tied to IPD-IMGT/HLA release version
	XX codes	c	versionless, but usage may be tied to IPD-IMGT/HLA release version
`kir`	IPD-KIR	d	tied to IPD-KIR release version

a. https://www.ebi.ac.uk/ipd/imgt/hla
b. https://bioinformatics.bethematchclinical.org/hla-resources/allele-codes/allele-code-lists
c. https://doi.org/10.1038/sj.bmt.1705672, XX Codes
d. https://www.ebi.ac.uk/ipd/kir

Version or date

The second field of the GL String Code contains the version of the base nomenclature of the gene family namespace. When the version is not available, the date when the GL String was constructed is used. This reflects the most recent version possible of the nomenclature. This field is not optional.

Version

When available, the version of the base nomenclature release is preferred over the date. A fully qualified version should be used (e.g., 3.33.0 vs 3.33).

Version examples:

3.20.0
3.25.0

Date

If using the date, the format must be as described for the HL7 FHIR date type (https://hl7.org/fhir/datatypes.html#date). Briefly,

A date, or partial date (e.g. just year or year + month) as used in human communication. There is no time zone. Dates SHALL be valid dates.
Regex: -?[0-9]{4}(-(0[1-9]|1[0-2])(-(0[0-9]|[1-2][0-9]|3[0-1]))?)?

Date examples:

2017-10-15
2015-01
2018

Genotype List String (GL String)

The GL String format uses a hierarchical set of operators to describe the relationships between alleles, lists of possible alleles, phased alleles, genotypes, lists of possible genotypes, and multilocus unphased genotypes, without losing typing information or increasing typing ambiguity.

The GL String version 1.1 grammar is described in
Genotype List String 1.1: Extending the Genotype List String grammar for describing HLA and Killer-cell Immunoglobulin-like Receptor genotypes. HLA. 2023 Aug;102(2):206-12. doi: 10.1111/tan.15126.

GL String delimiters & precedence

Precedence	Delimiter	Description
0	`?`	Possible Gene Locations describes locus ambiguity where the typing system cannot distinguish paralogous genes
1	`^`	Gene/Locus locus delimiter for multilocus unphased genotypes
2	`\|`	Genotype List describes genotype ambiguity where the typing system cannot distinguish chromosomal phase
3	`+`	Genotype
4	`~`	Haplotype indicates alleles that are in chromosomal phase (cis)
5	`/`	Allele List describes allele ambiguity where the typing system cannot distinguish between alleles

GL String parsing

GL String Components of a Multilocus Unphased Genotype (MUG) Parsing of GL String delimiters in a multilocus unphased genotype

GL String examples

HLA-A genotype with ambiguous allele
- HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:02:01:01
HLA-A ambiguous genotype
- HLA-A*01:02+HLA-A*03:02:01|HLA-A*01:03:01:01+HLA-A*03:04:01
HLA-DR haplotype
- HLA-DRB1*03:01:02~HLA-DRB5*01:01:01
HLA multi-locus unphased genotype
- HLA-A*02:302+HLA-A*23:26/HLA-A*23:39^HLA-B*44:02:13+HLA-B*49:08
KIR ambiguous genotype
- KIR3DL2*001+KIR3DL2*007|KIR3DL2*006+KIR3DL2*010
KIR locus ambiguity
- KIR2DL5A*0010101+KIR2DL5A*0010201?KIR2DL5B*0010201+KIR2DL5B*0010301

GL String Code Examples

Base nomenclature only

hla#3.25.0#HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:02:01:01
hla#3.29.0#HLA-DRB1*03:01:02~HLA-DRB5*01:01:01
hla#3.33.0#HLA-A*02:69+HLA-A*23:30|HLA-A*02:302+HLA-A*23:26/HLA-A*23:39
hla#2018-06#HLA-A*02:69+HLA-A*23:30
kir#2.3#KIR3DL2*001+KIR3DL2*007|KIR3DL2*006+KIR3DL2*010
kir#2.12#KIR2DL5A*0010101+KIR2DL5A*0010201?KIR2DL5B*0010201+KIR2DL5B*0010301

NMDP Multiple Allele Code (MAC) Designations

hla#2018-03-01#HLA-DPB1*04:ANKZX+HLA-DPB1*04:FNVS

MAC and WMDA extensions

hla#3.25.0#HLA-DPB1*04:ANKZX+HLA-DPB1*04:FNVS^HLA-DRB3*XXXX

as a valueCodeableConcept.coding within a HL7 FHIR Observation…

<valueCodeableConcept>
  <coding>
    <system value="http://glstring.org"/>
    <version value="1.1"/>
    <code value="hla#3.25.0#HLA-A*01:01:01:01/HLA-A*01:02+HLA-A*24:02:01:01"/>
  </coding>
</valueCodeableConcept>

References & Links

The genotype list string code syntax for exchanging nomenclature-level genotyping results in clinical and research data management and analysis systems. HLA. 2023 Oct;102(4):501-7. doi: 10.1111/tan.15145.

Genotype List String 1.1: Extending the Genotype List String grammar for describing HLA and Killer-cell Immunoglobulin-like Receptor genotypes. HLA. 2023 Aug;102(2):206-12. doi: 10.1111/tan.15126.

Genotype List String: a grammar for describing HLA and KIR genotyping results in a text string. Tissue Antigens. 2013 Aug;82(2):106-12. doi: 10.1111/tan.12150.

World Marrow Donor Association guidelines for use of HLA nomenclature and its validation in the data exchange among hematopoietic stem cell donor registries and cord blood banks. Bone Marrow Transplant. 2007 Jun;39(12):737-41. doi: 10.1038/sj.bmt.1705672.

IPD-IMGT/HLA Database
https://www.ebi.ac.uk/ipd/imgt/hla

IPD-KIR Database
https://www.ebi.ac.uk/ipd/kir

NMDP Multiple Allele Codes
https://bioinformatics.bethematchclinical.org/hla-resources/allele-codes/allele-code-lists

NMDP MAC Service UI
https://hml.nmdp.org/MacUI