Minimum information for reporting next generation sequence genotyping (MIRING): Guidelines for reporting HLA and KIR genotyping via next generation sequencing

• Published in: Human immunology Vol. 76; no. 12; pp. 954 - 962
• Main Authors: Mack, Steven J, Milius, Robert P, Gifford, Benjamin D, Sauter, Jürgen, Hofmann, Jan, Osoegawa, Kazutoyo, Robinson, James, Groeneweg, Mathijs, Turenchalk, Gregory S, Adai, Alex, Holcomb, Cherie, Rozemuller, Erik H, Penning, Maarten T, Heuer, Michael L, Wang, Chunlin, Salit, Marc L, Schmidt, Alexander H, Parham, Peter R, Müller, Carlheinz, Hague, Tim, Fischer, Gottfried, Fernandez-Viňa, Marcelo, Hollenbach, Jill A, Norman, Paul J, Maiers, Martin
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01-12-2015
• Subjects: Allergy and Immunology; Data standards; Genotyping; Genotyping Techniques; Guidelines as Topic; High-Throughput Nucleotide Sequencing - methods; High-Throughput Nucleotide Sequencing - standards; Histocompatibility Testing; HLA; HLA Antigens - genetics; Humans; KIR; MIRING; NGS; Potassium Channels, Inwardly Rectifying - genetics; Research Report - standards; consensus sequence block; International Organization for Standardization; GTR; Personal Information Protection and Electronic Documents Act; PIPEDA; IUBMB; European Molecular Biology Laboratory; sequence-specific oligonucleotide probe; NCBI; Genetic Testing Registry; Sequence Read Archive; uniform resource identifier; Genotype and Phenotype database; human leukocyte antigen; IEC; International HLA and Immunogenetics Workshop; OID; immuno polymorphism database; HIEDFS; IHIW; sequence-specific priming; International Nucleotide Sequence Database Collaboration; MIBBI; IMGT; Genotyping; KIR; International Union of Pure and Applied Chemistry; Sanger sequencing based typing; VCF; ENA; GRC; NGS; HLA; International Electrotechnical Commission; Health Insurance Portability and Accountability Act; Genome Reference Consortium; National Center for Biotechnology Information; SRA; variant call format; immunogenetics; killer-cell immunoglobulin-like receptor; Data standards; Immunogenomic Next Generation Sequencing Data Consortium; URI; EMBL; SFF; binary alignment/map; CSB; dbGAP; HIPAA; Immunogenomic Data Analysis Working Group; MIRING; HLA Information Exchange Data Format Standards; organization identifier; International Union of Biochemistry and Molecular Biology; INSDC; ISO; SBT; GL; next generation sequencing; SSOP; Minimum Information for Biological and Biomedical Investigations; IUPAC; Minimum Information for Reporting Immunogenomic NGS Genotyping; BAM; INGSDC; Genotype List; SSP; IDAWG; standard flowgram format; European Nucleotide Archive; IPD
• ISSN: 0198-8859; 1879-1166
• DOI: 10.1016/j.humimm.2015.09.011

Abstract The development of next-generation sequencing (NGS) technologies for HLA and KIR genotyping is rapidly advancing knowledge of genetic variation of these highly polymorphic loci. NGS genotyping is poised to replace older methods for clinical use, but standard methods for reporting and exchanging these new, high quality genotype data are needed. The Immunogenomic NGS Consortium, a broad collaboration of histocompatibility and immunogenetics clinicians, researchers, instrument manufacturers and software developers, has developed the Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines. MIRING is a checklist that specifies the content of NGS genotyping results as well as a set of messaging guidelines for reporting the results. A MIRING message includes five categories of structured information – message annotation, reference context, full genotype, consensus sequence and novel polymorphism – and references to three categories of accessory information – NGS platform documentation, read processing documentation and primary data. These eight categories of information ensure the long-term portability and broad application of this NGS data for all current histocompatibility and immunogenetics use cases. In addition, MIRING can be extended to allow the reporting of genotype data generated using pre-NGS technologies. Because genotyping results reported using MIRING are easily updated in accordance with reference and nomenclature databases, MIRING represents a bold departure from previous methods of reporting HLA and KIR genotyping results, which have provided static and less-portable data. More information about MIRING can be found online at miring.immunogenomics.org.