HML

NMDP^SM is committed to eliminating barriers to unrelated allogeneic hematopoietic cell transplantation (HCT). One issue in the HCT process is the extended time necessary to identify an appropriately matched donor.

Currently, the low/intermediate resolution human leukocyte antigen (HLA) typing results in the NMDP Registry^SM of potential volunteer donors 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). In collaboration with the HCT community, it is NMDP’s desire to reduce search times by optimizing primary data and result collection formats from all HLA typing laboratories.

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. However, 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.

What 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.

Find the complete schema specification for HML version 1.0 with examples at http://schemas.nmdp.org/.

Developers who are interested in participating in the continuing development of HML should 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:

HML Data Dictionary (PDF)

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.

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