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

Robert P. Milius, Michael Heuer, Daniel Valiga, Kathryn J. Doroschak, Caleb J. Kennedy, Yung –Tsi Bolon, Joel Schneider, Jane Pollack, Hwa Ran Kim, Nezih Cereb, Jill A. Hollenbach, Steven J. Mack, Martin Maiers
doi: https://doi.org/10.1101/014951
Robert P. Milius
1National Marrow Donor Program, MN USA
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Michael Heuer
1National Marrow Donor Program, MN USA
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Daniel Valiga
1National Marrow Donor Program, MN USA
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Kathryn J. Doroschak
1National Marrow Donor Program, MN USA
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Caleb J. Kennedy
1National Marrow Donor Program, MN USA
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Yung –Tsi Bolon
1National Marrow Donor Program, MN USA
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Joel Schneider
1National Marrow Donor Program, MN USA
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Jane Pollack
1National Marrow Donor Program, MN USA
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Hwa Ran Kim
2HistoGenetics LLC, USA
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Nezih Cereb
2HistoGenetics LLC, USA
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Jill A. Hollenbach
3University of California – San Francisco
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Steven J. Mack
4Children’s Hospital & Research Center Oakland, Oakland, CA, USA
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Martin Maiers
1National Marrow Donor Program, MN USA
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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.

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 Receptor
MHC
Major Histocompatibility Complex
MIRING
Minimum Information for Reporting Immunogenomic NGS Genotyping
NCI
National Cancer Institute
NGS
Next Generation Sequencing
NMDP
National Marrow Donor Program
OID
Object Identifier
SBT
Sequence Based Typing
SSO
Sequence Specific Oligonucleotide
SSP
Sequence Specific Primer
URI
Uniform Resource Identifier
XML
eXtensible Markup Language
Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 06, 2015.
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Histoimmunogenetics Markup Language 1.0: Reporting Next Generation Sequencing-based HLA and KIR Genotyping
Robert P. Milius, Michael Heuer, Daniel Valiga, Kathryn J. Doroschak, Caleb J. Kennedy, Yung –Tsi Bolon, Joel Schneider, Jane Pollack, Hwa Ran Kim, Nezih Cereb, Jill A. Hollenbach, Steven J. Mack, Martin Maiers
bioRxiv 014951; doi: https://doi.org/10.1101/014951
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Histoimmunogenetics Markup Language 1.0: Reporting Next Generation Sequencing-based HLA and KIR Genotyping
Robert P. Milius, Michael Heuer, Daniel Valiga, Kathryn J. Doroschak, Caleb J. Kennedy, Yung –Tsi Bolon, Joel Schneider, Jane Pollack, Hwa Ran Kim, Nezih Cereb, Jill A. Hollenbach, Steven J. Mack, Martin Maiers
bioRxiv 014951; doi: https://doi.org/10.1101/014951

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