HLA Twin™

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Product Sheets and Technical Documents
Release Notes

Omixon HLA Twin CE 4.1.0

    The software has gone through a major overhaul providing a more responsive and comfortable experience. This includes:
New features:
  • Serological equivalents and Bw4/Bw6 reporting for allele pairs
  • New novel allele export feature with table file export for easier submission of novel alleles to GeneBank and IMGT
  • PIRCHE epitope matching integration
  • Sample files now can be sorted by their sample/index number (S1, S2, etc...)
  • A new Typer Scheduler window was introduced that allows the user to change the order of scheduled analyses of samples
  • Algorithmic tweaks providing about 25% faster analysis time per sample
  • A more robust database solution for better performance (MySQL)
  • Faster folder loading
  • Better response times between folders and screens
  • Improved and more reliable server-client connection
  • An improved automated analysis method
  • The Genotyping analysis result and Genotyping sample result screens were redesigned for more intuitive display of results, especially designed to handle the increasing the 4th field ambiguity rates caused by the expanding IMGT database
  • New distributed typer scheme
Bug fixes:
  • Memory-related issues which caused the server to crash have been fixed
  • HPRIM export-related issues have been fixed
  • "Too ambiguous to report" message in the PDF export has been removed and an extended number of allele pairs are listed instead
  • A bug where specific DQB1 alleles were not viewable in the Genome browser has been fixed

Omixon HLA Twin RUO 4.1.0

Improvements and fixes:

  • Algorithmic tweaks providing about 25% faster analysis times per sample
  • Approved results can be exported successfully
  • The Setup Loci options now will not change automatically

New features:

  • Serological equivalents and Bw4/Bw6 reporting for allele pairs
  • New novel allele export feature with table file export for easier submission of novel alleles
  • Sample files now can be sorted by their sample number (S1, S2, etc...)

Omixon HLA Twin RUO 4.0.1

Improvements and fixes:

  • A more reliable database solution was implemented
  • The logic behind the automated analysis was improved
  • Bugs in the genotyping dashboard were fixed
  • Minor problems with the installer were fixed

Omixon HLA Twin RUO 4.0.0

New features:

  • Automated analysis support for the new Illumina Local Run Manager software running on MiSeq and MiniSeq sequencers

Other technical improvements and fixes:

  • New user interface layout with improved response times
  • A new and more robust distributed typer configuration
  • The order of the samples scheduled for analysis can be rearranged
  • External SQL database support
  • New licensing system

Omixon HLA Twin RUO 3.1.3

New features:

  • PIRCHE epitope matching integration

Other technical improvements and fixes:

  • Reporting and genotyping performance improvement when using remote work folder

Omixon HLA Twin CE 3.1.1

New features:

  • V3.0 assay support
  • ABO and MICA genotyping support
  • New allele database structure and format
  • New QC metric to assess the number of novel positions

Other technical improvements and fixes:

  • Overall faster response between pages
  • Sample folder loading speed-up
  • Memory handling refinements and improvements
  • Increased stability when more read data is analyzed
  • Temporary folder cleanup refinement
  • Exporting related fixes and improvements

Omixon HLA Twin RUO 3.1.1

New feature:

  • New QC metric to assess the number of novel positions

Other technical improvements and fixes:

  • Overall faster response between pages
  • Memory handling refinements and improvements
  • Exporting related fixes and improvements

Omixon HLA Twin RUO 3.1.0

User interface performance improvements:

  • Overall faster response between pages
  • Sample folder loading speed-up

Other technical improvements:

  • Memory leak patch
  • Memory handling scheme change
  • Increased stability when more read data is analyzed
  • Temporary file cleanup refinement

Omixon HLA Twin RUO 3.0.0

  • V3.0 assay support
  • Whole gene analysis for Statistical Genotyping
  • ABO and MICA genotyping support
  • New allele database structure and format

Omixon HLA Twin CE/RUO 2.5.1

  • Spot noise ratio calculation redefined.
  • Spot noise ration thresholds were refined.
  • Improved client response in server-client installations.
  • Minor refinements in HPRIM export format.

Omixon HLA Twin CE/RUO 2.5.0

New features and improvements

  • Holotype HLA v2 kit support: Assay version selector allows user to select the right assay version for analysis.
  • IMGT/HLA database version was released:
    • HLA-DRB1*09:01:02 allele extension was removed
    • Erroneous HLA-DRB1*14:13 allele sequence was replaced with record from IMGT/HLA 3.30.0
    • The database was validated with the following software versions: Omixon HLA Twin 2.1.3 CE & RUO, Omixon HLA Twin 2.1.4 CE & RUO and Omixon HLA Twin 2.5.0 RUO. For other software versions, each laboratory is advised to do its own internal validation.
  • Distributed typing service allows for batch analysis and filtering tasks to run in parallel in a client-server environment
  • Existing user accounts cannot be deleted through the UI; administrators have the option to disable and reactivate them whenever needed
  • New export options:
    • JSON export for result files
    • Fasta export for consensus sequences
    • Export result files to PDF/HML with or without LD data
  • Re-Analyse button for result files added
  • Improved automated analysis options: predefined time values for triggering analysis
  • File system access rights are now considered on the HLA Typing dashboard: inaccessible folders are marked red and cannot be clicked
  • Pause/resume option for analysis tasks was removed from client-server installations
  • Improved “Targeted Gene List” loading when configuring analysis


  • Algorithm improvement to fix reported false allele calls
  • Spot noise calculation was fixed for reported special cases
  • Temporary file cleanup fix to avoid losing files still in use
  • Fix for inconsistent display of missing genotype markups
  • Amino acid track fixes for special cases
  • HML export fix: best matching alleles are always exported now
  • Genome browser bug resulting in "rainbow effect"
  • Continuous consensus QC metric corrected
  • Bugs related to result approval were fixed:
    • Commenting on approved results isn't possible any more
    • Result approval buttons work consistently with all precision settings

Omixon HLA Twin RUO 2.2

Bugfixes and improvements

  • User details are now filled out correctly in the PDF report for results produced with automated analyses
  • New read mapping options introduced (skip read mapping, map reads to result alleles only or map reads to all alleles)
  • Read mapping information and targeted gene set added to analysis tooltips on the HLA typing dashboard
  • Imbalanced best matching allele results produced by a statistical-only analysis are now shown correctly
  • New hydrophobicity  based color scheme for the amino acid track in the HLA browser
  • HLA browser now jumps to the first best matching pair instead of the first allele pair
  • Error details can now be copied to the clipboard from the task manager
  • Application settings dashboard side panel reorganized


Analysis results produced with a software version 2.2.0 or higher cannot be viewed in the genome browser with software versions prior to v2.2.0.


The following genotyping performance improvements were measured compared to v2.1.4:

Input data set Benchmark result
96 samples   7 loci/300 chem. 715 -> 593 sec/sample, total 15 hours,    17% improvement
96 samples   7 loci/500 chem. 646 -> 514 sec/sample, total 12.7 hours, 21% improvement
96 samples 11 loci/300 chem. 924 -> 767 sec/sample, total 19 hours,    17% improvement
96 samples 11 loci/500 chem. 899 -> 691 sec/sample, total 17 hours,    23% improvement

Benchmarking environment:

  • CPU: 8 CPU - Intel(R) Quad Core(TM) i7-4770 CPU @ 3.40GHz (+all Cores are used)
  • Memory: 24 GB JVM heap
  • OS: Windows

Omixon HLA Twin RUO & CE 2.1.4

Bugfixes and improvements 

  • QC result calculation for key exon mismatch count fixed
  • HML export related changes:
    • Variant reporting can be turned on/off
    • Novel allele postfix can be trimmed without trimming the allele name
    • Export now works for newer IMGT/HLA database versions (version 3.26.0 and above)
    • Novel allele postfixes are now exported correctly

Omixon HLA Twin RUO & CE 2.1.3

Improvements and bug fixes
  • IMGT/HLA 3.28.0 released

Omixon HLA Twin RUO 2.1.2

Improvements and bug fixes
  • HML export bug fixes and improvements
    • New pairwise alignment base variant generation method
    • Improved reference selection:
      • For not fully defined best matching alleles, the closest fully defined alleles are used as references
      • For novel allele results, the base allele is used as a reference
    • Loci with no allele calls are no longer exported
  • Consistent naming convention for extended allele handling
  • Targeted locus list handling fixed in protocols
  • Temp folder is now created by the application if a non-existing folder was specified during installation
  • Null alleles and novel alleles no longer get trimmed in low resolution PDF and HML exports
  • Temporary file cleanup improved

Omixon HLA Twin RUO 2.1.1

  • Performance problem fix - Fixes the performance problems reported by some of our customers since the release of Twin 2.1.0.
  • Temporary folder cleanup fix - Fixes the bug where on some occasions the temporary files generated during the analyses are not deleted until the Twin Serve/Desktop is restarted, leading to excess disk space consumption.

Omixon HLA Twin RUO 2.1

  • HLA browser improvements
    • Faster browsing - much improved loading speed of HLA browser
    • Fixed some visualisation issues with misaligned exons
    • Context sensitive guide for the HLA browser
  • Linkage Disequilibrium (LD) improvements
    • Extended LD checks to cover DQB1 and DQA1 in addition to DRB3/4/5
    • Fixed known display issues with DRB3/4/5 results
  • Improved memory settings
    • On first use popup, warning if insufficient memory configured
    • Recommendation for memory settings on installation
  • User interface performance improvement
    • Faster responses from user interface when analyses are running

Omixon HLA Twin RUO

  • Noise filter improvements to improve genotyping results on DRB3 and DRB5
  • Linkage disequilibrium based result interpretation and annotation improvements
  • Server automation stability and performance improvements
  • Several other small bug fixes

Omixon HLA Twin RUO 

  • Linkage disequilibrium based result interpretation and annotation fixes
  • Separated QC metrics for allele imbalance in the exon and non-exon regions
  • Option to add custom hemizygous genotype
  • Fixed HML export to consider phasing in the sequence tags
  • Fixed empty result presentation for loci without data
  • Fixed product name in the installer file name
  • Increased maximum memory setup limit to 512GB

Omixon HLA Twin RUO 

  • Analysis improvements
    • Resolution of DRB4*01:03:01:02N by allele database extension
    • Better crossmapping detection on DRB loci
  • Reporting improvements
    • Reporting difference between homozygous and hemizygous DRB results based on linkage disequilibrium information in publicly available databases
    • Dropout cause resolution supporting hints for loci with missing genotype
    • Allele frequency reporting based on the database of www.allelefrequencies.net
  • Usability improvements
    • Notification about new IMGT/HLA database availability
    • Higher quality sequence alignments in the genome browser
    • Better loading performance for the genome browser
  • Several bug fixes

Omixon HLA Twin RUO & CE

  • Non-exon spot noise ratio QC metric's info threshold raised up to 20% to be not as stringent as previously
  • Spot noise ratio QC metric for consensus regions where no allele annotation is present in the first best allele pair is not counted from now on to be not as stringent as previously
  • File browser bug has been fixed for mixed Windows-Linux client-server installations
  • Browsing results approved with version prior to 1.1.2 has been fixed

Omixon HLA Twin RUO

  • New exon/non-exon spot noise ratio quality control metrics for more robust contamination detection
  • Minor fixes in the HML export

Omixon HLA Twin RUO

  • Fixed proprietary internal filtering database to improve genotyping and consensus building quality on HLA-DPA1 and HLA-DRB5
  • Minor fixes in the HML export

Omixon HLA Twin RUO

  • Upgrade installation fixes
    • Fixed upgrade installation issue on Mac OS X
    • Logs are no longer removed during upgrade installation
    • RUO and CE cross-upgrade installation is now possible from Twin version 1.1.2
    • Accidental upgrade from Twin to Explore is no longer possible
  • Genome browser fixes
    • Multiple minor issues resolved for the variant relationship track
    • Gap visualization issues corrected in the sequence displays
  • Logout issue when connection to server was lost has been fixed
  • Image display fixed in the help
  • Result loading performance issue has been resolved

Omixon HLA Twin RUO 1.1.3

  • The HLA typing software for research and discovery
    • Flexible and customizable to handle various sequencing data types, i.e. targeted, whole exome or whole genome
    • Includes both genotyping algorithms
  • Analysis improvements
    • 150bp chemistry support
    • Improved novel allele detection
    • Better crossmapping detection
  • Usability improvements
    • Genotype editor
    • Variant phasing track in the genome browser
    • Base statistics visualization in the genome browser
    • Improved visibility of allele assignments
    • Configurable data and result folders for better analysis result organization
    • Optional secondary genotyping method execution based on QC results for performance improvement
    • Scalable window contents to support very large and small resolution displays
  • Research use only edition - no compliance restrictions
    • Custom analysis can be configured without a notification
    • No audit related restrictions
  • Export improvements
    • Optional precision reduction in the HML export
    • Variant and novelty reporting in the HML export
  • Various usability improvements and bugfixes

Example Data Set

MyHolotype / Identification Required

Please sign up for MyHolotype to get more information about:

- Handbooks

- Instructions for Use

- Example Data Sets for Special Cases

- Workbooks for Self-driven Trainings

- IMGT HLA database bundles

Example Data Sets for Special Cases