HML


HML

Histoimmunogenetics Markup Language


Background

The National Marrow Donor Program® (NMDP) is a Registry of over seven million potential volunteer donors. We are committed to eliminating barriers to unrelated stem cell transplantation (USCT). One of the outstanding issues in the USCT process is the extended time necessary to identify an appropriately matched donor. Currently, the low/intermediate resolution HLA typing results in the NMDP Registry are condensed to allele codes, which can decrease the specificity of the typing and result in increased numbers of donors appearing as potential matches. In many cases, this translates into longer search times and additional costs for further HLA testing to find a suitable donor. The collection and utilization of primary HLA typing data could alleviate this issue through analysis of the true patterns of polymorphism underlying the coded results (Rev. Immunogenet. 2000;2(4):449-60 1). It is the desire of the NMDP, in collaboration with the USCT community, to reduce search times by optimizing primary data and result collection formats from all HLA typing laboratories.

In order to facilitate the electronic reporting of HLA testing results and the collection of the raw probe, primer and sequence data, the NMDP Bioinformatics group developed a software reporting format in 1998 but maintenance and extension became increasingly difficult due to the rigid format limitations. Therefore, the NMDP Bioinformatics group developed an XML-based reporting format to address the shortcomings of the previous format. The XML-based format is called Histoimmunogenetics Markup Language (HML) and is intended as a potentially general-purpose format for exchanging genetic typing data.


HML supports:

  • HML version 1.0  supports
    • all features from HML version 0.3.3 listed below and new features including
    • NGS based genotyping methods,
    • external references to raw sequence reads, registered methodologies, and reference data,
    • complete reporting of allele and genotype ambiguity through the use of GL Strings, and
    • MIRING compliant reporting.

The complete schema specification for HML version 1.0 with examples is found at http://schemas.nmdp.org/.

Developers who are interested in participating in the continuing development of HML, please visit https://github.com/nmdp-bioinformatics/hml.

  • HML version 0.3.3 supports
    • Reporting of paired genotype allele lists as determined from Primary DNA Results (SSO, SSP and SBT)
    • Reporting genetic typing results using WHO nomenclature, and/or
    • Describing the results of any/all tests performed to generate genetic typing results (raw data). These tests include:
      • Sequence Specific Oligonucleotide Probing
      • Sequence Specific Primer Amplification
      • Sequence Based Typing
      • Reference Strand Conformational Analysis

The data dictionary document for HML version 0.3.3 provides a single convenient and comprehensive reference.

The complete schema specification for HML version 0.3.3 is also found at http://schemas.nmdp.org/, as are schemas for some older deprecated versions.

Note: NMDP is continuing to improve HML. Please contact us if you would like to help pilot submission and improvements of this format. (Contact mmaiers@nmdp.org )