Histoimmunogenetics Markup Language (HML)

Background

The National Marrow Donor Program^® (NMDP) is a Registry of over five 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.

To facilitate the electronic reporting of HLA testing results and the collection of the raw probe and primer data, the NMDP Bioinformatics group developed the Laboratory Software (LBSW) reporting format. LBSW was originally developed for the collection of typing data destined for the NMDP Registry, but has been adapted to additional higher resolution typing projects. LBSW has been expanded and modified as the NMDP has attempted to capture more complex data, such as multiple tests performed on a single sample, typings utilizing multiple methodologies and tests of genetic loci other than HLA. However, LBSW's rigid format limitations make maintenance and extension increasingly difficult. Therefore, the NMDP Bioinformatics group has developed a new XML-based reporting format to address the shortcomings of the LBSW format.

Overview of HML

The NMDP Bioinformatics group has developed an XML-based format called HML. The HML format is intended not only as a replacement for LBSW, but as a potentially general-purpose format for exchanging genetic typing data.

HML supports:

HML version 0.3 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

HML Versions

Details about each HML version are available at the links listed below. Please send all questions and comments to
hml-comments@nmdp.org.

NEW - HML Version 0.3

Version 0.3 Examples and DTD.

HML Version 0.2

Version 0.2 Examples and DTD.

HML Version 0.1

Downloads

Document Type Definition 0.1 (DTD)

Information about DTDs and XML in general may be found on the W3C Web site at http://www.w3c.org/XML.

References:

Rev Immunogenet 2000;2(4):449-60 www.ncbi.nlm.nih.gov/entrez/query.fcgi

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HML Version 0.3 HML Version 0.2	Histoimmunogenetics Markup Language (HML) Background The National Marrow Donor Program^® (NMDP) is a Registry of over five 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. To facilitate the electronic reporting of HLA testing results and the collection of the raw probe and primer data, the NMDP Bioinformatics group developed the Laboratory Software (LBSW) reporting format. LBSW was originally developed for the collection of typing data destined for the NMDP Registry, but has been adapted to additional higher resolution typing projects. LBSW has been expanded and modified as the NMDP has attempted to capture more complex data, such as multiple tests performed on a single sample, typings utilizing multiple methodologies and tests of genetic loci other than HLA. However, LBSW's rigid format limitations make maintenance and extension increasingly difficult. Therefore, the NMDP Bioinformatics group has developed a new XML-based reporting format to address the shortcomings of the LBSW format. Overview of HML The NMDP Bioinformatics group has developed an XML-based format called HML. The HML format is intended not only as a replacement for LBSW, but as a potentially general-purpose format for exchanging genetic typing data. HML supports: HML version 0.3 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 HML Versions Details about each HML version are available at the links listed below. Please send all questions and comments to hml-comments@nmdp.org. NEW - HML Version 0.3 Version 0.3 Examples and DTD. HML Version 0.2 Version 0.2 Examples and DTD. HML Version 0.1 Downloads Document Type Definition 0.1 (DTD) Information about DTDs and XML in general may be found on the W3C Web site at http://www.w3c.org/XML. References: Rev Immunogenet 2000;2(4):449-60 www.ncbi.nlm.nih.gov/entrez/query.fcgi

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