The genotype list string code syntax for exchanging nomenclature‐level genotyping results in clinical and research data management and analysis systems
Abstract
The nomenclatures used to describe HLA and killer‐cell immunoglobulin‐like receptor (KIR) alleles distinguish unique nucleotide and peptide sequences, and patterns of expression, but are insufficient for describing genotyping results, as description of ambiguities and relations across loci require terminology beyond allele names. The genotype list (GL) String grammar describes genotyping results for genetic systems with defined nomenclatures, like HLA and KIR, documenting what is known and unknown about a given genotyping result. However, the accuracy of a GL String is dependent on the reference database version under which it was generated. Here, we describe the GL string code (GLSC) system, which associates each GL String with meta‐data describing the specific reference context in which the GL String was created, and in which it should be interpreted. GLSC is a defined syntax for exchanging GL Strings in the context of a specific gene‐family namespace, allele‐name code‐system, and pertinent reference database version. GLSC allows HLA and KIR genotyping data to be transmitted, parsed and interpreted in the appropriate context, in an unambiguous manner, on modern data‐systems, including Health Level 7 Fast Healthcare Interoperability Resource systems. Technical specification for GLSC can be found at https://glstring.org.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jul 05, 2023
- Source ID
- 10.1111/tan.15145
Entities
People
- James Robinson
- Joel Schneider
- Jürgen Sauter
- Kazutoyo Osoegawa
- Lloyd Mckenzie
- Martin Maiers
- Robert P. Milius
- Steven Mack
Organizations
- DKMS Donor Center gGmbH
- National Institute of Allergy and Infectious Diseases
- National Marrow Donor Program
- Office of Naval Research
- Office of the National Coordinator for Health Information Technology
- Stanford University
- University College London
- University of California, San Francisco