Histoimmunogenetics Markup Language 1.0: Reporting Next Generation Sequencing-Based HLA and KIR Genotyping

Hum Immunol. 2015 Dec;76(12):963-74. doi: 10.1016/j.humimm.2015.08.001. Epub 2015 Aug 28.

Abstract

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.

Keywords: Data standards; Genotyping; HLA; HML; KIR; MIRING; NGS.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Alleles
  • Computational Biology / methods
  • Computational Biology / standards
  • Database Management Systems
  • Genotype
  • Genotyping Techniques*
  • HLA Antigens / genetics*
  • High-Throughput Nucleotide Sequencing*
  • Histocompatibility Testing*
  • Humans
  • Potassium Channels, Inwardly Rectifying / genetics*
  • Reproducibility of Results
  • Research Report / standards*
  • Sequence Analysis, DNA
  • Software*

Substances

  • HLA Antigens
  • Potassium Channels, Inwardly Rectifying