Omixon Holotype HLA validation Alpha Study featured at ASHI Annual Meeting 2014

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Holotype HLA and other Omixon products are featured across multiple sessions at the ASHI Annual Meeting 2014 in Denver Colorado 20-24 October.

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No discordance between the per-locus and per-sample indexing strategies have been reported among more than 500 routine clinical NGS samples with Holotype HLA

Global biotechnology company Omixon, headquartered in Budapest with US offices in Cambridge, MA, announce today that Holotype HLA™ and other Omixon products will be featured in five posters and three oral presentations at the annual meeting of the American Society for Histocompatibility and Immunogenetics (ASHI) held from October 20-24 in Denver, CO. In the session entitled “New and Improved NGS” (Oct 21, 2:00-3:30pm), Deborah Ferriola from The Children’s Hospital of Philadelphia (CHOP) will present “A multi-center study using Next-Generation Sequencing (NGS) for HLA Genotyping”, a talk that focuses on the NGS-based HLA genotyping assay that is now in routine clinical practice at CHOP, and for which Omixon owns the worldwide exclusive license on the Illumina platform. The assay is combined with Omixon HLA Twin™, the only software that determines HLA genotypes from NGS data with two orthogonal algorithms, and this combination product is now marketed and sold globally as Omixon Holotype HLA.

Of particular interest in Ferriola’s presentation is the six-participant, double-blind Alpha Study, a level of validation of NGS for HLA genotyping that sets Holotype HLA strides ahead of competitors both on the MiSeq platform and on other NGS instruments. In this Alpha Study, the same 16 samples were genotyped using Holotype HLA at HLA-A, B, C, DRB1, and DQB1 by each of the six participating labs. Two indexing strategies, locus-specific indexing and per-sample indexing, were compared in order to successfully validate the pooling of MHC Class I and Class II loci that is a unique feature of the Holotype HLA assay. Sequence analysis and genotyping was performed using Omixon HLA Target. In the locus-specific indexing strategy, Omixon Target HLA was able to determine the genotypes with 100% accuracy, while in the per-sample indexing strategy, it was able to determine the genotypes with 99.5% accuracy. Reproducibility between laboratories was 99.7%, with the only cause of discordance between labs being a cross-contamination of a single amplicon that was identified by the unique gene-level QC reporting features of Omixon’s software.

Since the conclusion of the Alpha Study, Omixon has formally announced its launch of Holotype HLA via its Early Access Program. One key feature of that collaboration is the introduction of Omixon HLA Twin, the only software that determines HLA genotypes from NGS data with two orthogonal algorithms. When re-analyzing the Alpha Study data including the new de novo assembly-based Consensus Genotyping algorithm, the researchers at CHOP were able to improve on the 99.5% accuracy figure described in their original submission and successfully recover the remaining 0.5% of incorrect genotypes.

Of additional significance, 100% concordance was observed between the two indexing methodologies, which highlights a unique achievement in multiplexing Class I and Class II loci. No other method has successfully resolved the mixture of Class I and Class II data, positioning Holotype HLA as the only whole-gene NGS genotyping product for HLA capable of scaling to 96 samples per MiSeq run and 192 samples per run by 2015.

In addition to the Alpha Study data, as CHOP is the first hospital anywhere in the world to offer comprehensive HLA genotyping by NGS using Holotype HLA, over 500 samples have already been processed in routine clinical practice at the Monos lab at CHOP. Importantly, “No discordance between the per-locus and per-sample indexing strategies have been reported among those samples”, notes Dr. Attila Bérces, Chairman and Founder at Omixon. “This demonstrates that the per-sample indexing strategy for pooling Class I and Class II loci as pioneered in Holotype HLA provides an unparalleled value proposition to the HLA genotyping market in terms of throughput and quality.”

Oct 20-24, 9am-5pm | Omixon will be exhibiting at Booth #506 throughout the conference
Oct 20, 10am-1pm | Novel Allele Discovery Workshop with Omixon HLA Twin™
Oct 23, 12:30-2pm | Omixon Holotype HLA Lunch

Oct 21, 2pm | Deborah Ferriola - A multi-center study using Next-Generation Sequencing (NGS) for HLA Genotyping
OR04 Oct 22, 2:30 | Curt Lind - A Targeted Approach to Next-Generation HLA Sequencing
OR03 Kathleen Davis et al. - HLA-Genotyping of Clinical Specimens Using Ion Torrent-Based NGS
OR02 Yuki Ozaki et al. - Development of Advanced NGS based HLA DNA Typing Method SS-SBT
P059 | Szilveszter Juhos et al. - Meta analysis of sequence-based HLA typing approaches
P090 | Szilveszter Juhos et al. - Next Generation Sequencing-based HLA typing of saliva and blood samples from the same donors produces concordant typing results
P092 | Cassandra Jabara et al. - Performance evaluation of high resolution 11 loci HLA-typing prototype assay using NGS technology
P100 | Yuxin Yin - Long Range NGS HLA Typing is accurate in the identification of common, rare and novel alleles

Omixon is a privately held, global bioinformatics company, headquartered in Budapest, Hungary, that specializes in the analysis of targeted Next Generation Sequencing (NGS) data. Omixon Target™ HLA offers the most accurate high-resolution HLA genotyping software available. Omixon also helps scientists and clinicians to analyze the most challenging genomic regions including HLA. For more information, visit

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Peter Meintjes, PhD

Tim Hague
Omixon Biocomputing Solutions
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