Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping

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• 作者：Robert P. Milius^a ; ^{bmilius@nmdp.org" class="auth_mail" title="E-mail the corresponding author} ; Michael Heuer^a ; Daniel Valiga^a ; Kathryn J. Doroschak^a ; Caleb J. Kennedy^a ; Yung-Tsi Bolon^a ; Joel Schneider^a ; Jane Pollack^a ; Hwa Ran Kim^b ; Nezih Cereb^b ; Jill A. Hollenbach^c ; Steven J. Mack^d ; Martin Maiers^a
• 关键词：BRIDG ; Biomedical Research Integrated Domain Group ; CDISC ; Clinical Data Interchange Standards Consortium ; DaSH ; Data Standard Hackathon ; EMBL ; European Molecular Biology Laboratory ; ENA ; European Nucleotide Archive ; FDA ; Food and Drug Administration ; GL ; Genotype List ; HML ; Histoimmunogenetics Markup Language ; HLA ; Human Leucocyte Antigen ; IMGT ; ImMunoGeneTics ; ISO ; International Organization for Standardization ; LSDAM ; Life Sciences Domain Analysis Model ; KIR ; Killer-cell Immunoglobulin-like R
• 刊名：Human Immunology
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：76
• 期：12
• 页码：963-974
• 全文大小：1593 K

文摘

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.