NEW YORK (GenomeWeb) – Omixon today said it is collaborating with the Global Genomics Group to validate Omixon's Target HLA software to determine HLA genotypes from whole-genome sequencing datasets.
G3 will provide the whole-genome datasets and the corresponding DNA samples from 340 subjects enrolled in the Global Clinical Study, and Omixon will genotype the samples with its software and compare its results with Sanger sequence-based typing, the current gold standard, and targeted next-generation sequencing using its Holotype HLA assay for use on the Illumina MiSeq instrument.
Histogenetics will perform the Sanger sequence-based typing, while the Monos Lab at the Children's Hospital of Philadelphia will conduct the targeted HLS genotyping from NGS data.
Omixon was awarded a Small Business Research Initiative grant from Genomics England to help fund the project, which supports the development of new technologies for genomic sequence data analysis and interpretation as part of the 100,000 Genomes Project.
Omixon said that the HLA region on chromosome 6 has the highest density of disease association in the genome and HLA genotyping is the most frequently performed genetic test worldwide, with more than 4 million tests done each year. However, the HLA region is often omitted from whole-genome and whole-exome data analysis because of the difficulty involved in analyzing it.
Omixon's approach to overcoming this is to first map the whole-genome sequence data to the sequence database of all known HLA genotypes, instead of using a single human genome reference sequence. The second step involves ensuring algorithm scalability to whole-genome data.
"This SBRI grant from Genomics England and WGS datasets and corresponding DNA samples provided by G3 allows us to demonstrate to a peer-reviewed publication standard the scalability of our software to [whole-genome sequence] data and the concordance with both a targeted NGS approach and the gold standard Sanger" sequence-based typing, Omixon CEO Tim Hague said in statement.
If Omixon is successful in demonstrating the utility of its approach, it will genotype the G3 data with its HLA Twin software for determining HLA genotypes from NGS data using two orthogonal algorithms.