RT Journal Article
SR Electronic
T1 Histoimmunogenetics Markup Language 1.0: Reporting Next Generation Sequencing-based HLA and KIR Genotyping
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 014951
DO 10.1101/014951
A1 Milius, Robert P.
A1 Heuer, Michael
A1 Valiga, Daniel
A1 Doroschak, Kathryn J.
A1 Kennedy, Caleb J.
A1 Bolon, Yung –Tsi
A1 Schneider, Joel
A1 Pollack, Jane
A1 Kim, Hwa Ran
A1 Cereb, Nezih
A1 Hollenbach, Jill A.
A1 Mack, Steven J.
A1 Maiers, Martin
YR 2015
UL http://biorxiv.org/content/early/2015/02/06/014951.abstract
AB We present an electronic format for exchanging data for HLA and KIR genotyping with extensions for next-generation sequencing (NGS). This format addresses NGS data exchange by refining the Histoimmunogenetics Markup Language (HML) to conform to the proposed Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines (miring.immunogenomics.org). Our refinements of HML include two major additions. First, NGS is supported by new XML structures to capture additional NGS data and metadata required to produce a genotyping result, including analysis-dependent (dynamic) and method-dependent (static) components. A full genotype, consensus sequence, and the surrounding metadata are included directly, while the raw sequence reads and platform documentation are externally referenced. Second, genotype ambiguity is fully represented by integrating Genotype List Strings, which use a hierarchical set of delimiters to represent allele and genotype ambiguity in a complete and accurate fashion. HML also continues to enable the transmission of legacy methods (e.g. site-specific oligonucleotide, sequence-specific priming, and sequence based typing (SBT)), adding features such as allowing multiple group-specific sequencing primers, and fully leveraging techniques that combine multiple methods to obtain a single result, such as SBT integrated with NGS.BRIDGBiomedical Research Integrated Domain GroupCDISCClinical Data Interchange Standards ConsortiumDaSHData Standard HackathonEMBLEuropean Molecular Biology LaboratoryENAEuropean Nucleotide ArchiveFDAFood and Drug AdministrationGLGenotype ListHMLHistoimmunogenetics Markup LanguageHLAHuman Leucocyte AntigenIMGTImMunoGeneTicsISOInternational Organization for StandardizationLSDAMLife Sciences Domain Analysis ModelKIRKiller-cell Immunoglobulin-like ReceptorMHCMajor Histocompatibility ComplexMIRINGMinimum Information for Reporting Immunogenomic NGS GenotypingNCINational Cancer InstituteNGSNext Generation SequencingNMDPNational Marrow Donor ProgramOIDObject IdentifierSBTSequence Based TypingSSOSequence Specific OligonucleotideSSPSequence Specific PrimerURIUniform Resource IdentifierXMLeXtensible Markup Language