We are happy to let you know that a new version 1.8 of Omixon Target is now available, including updated features and further improvements.

Feel free to download the new version using the plugin on the Omixon website. When installing, select the ‘upgrade’ option to renew an existing installation. This will keep all existing credits and results.

If you have the server version of Omixon Target, our support team will contact you shortly with an update.

Major New Features for the HLA typing module

• Whole gene visualization
• Whole gene typing (beta feature)
• Novel allele detection, only for SNPs (beta feature)

Minor Improvements (HLA typing module)

• Homogeneous subsampling (optimization for non-randomly distributed input data)
• Quality based read trimming (quality improvement)
• Key exon based allele pre-filtering (bug fix and optimization)
• Genome browser improvements:
• Multiple sequence alignment of alleles for more useful visual comparison (new feature)
• More metadata for short reads (quality, sequence) in the display, plus a configuration mechanism (new feature)
• New context menus (right click on the tables or genome browser)
• Other minor bugfixes and improvements

Brief overview of existing and newly introduced alignment methods

• Exons Only method is the most suitable for high accuracy 6 digit typing, and only analyses the exonic regions from the IMGT/HLA database. It is equivalent to the default 6 digit typing mode from previous releases. Results visualization will also display the exons only. Novel information in introns will be ignored.
• Exons, Introns and UTRs method is the most suitable for high accuracy 8 digit typing, and will analyze other regions in addition to the exons, depending on what intronic and UTR info is in the database for each allele. It is equivalent to the default 8 digit typing mode from previous releases, and it is now no longer a beta feature. Each of these regions has the short read data aligned separately and the whole gene will be visible in the results.
• The new Whole Gene method is currently more for kit development and allele discovery rather than reliable high-throughput typing. It’s an experimental analysis mode that is being beta tested. In this case the short read data is aligned against the whole allele reference sequence, depending on what is in the database. It should provide more reliable novel SNP detection around intron/exon boundaries than the Exons, Introns and UTRs mode.

All alignment methods support the new, beta Novel Allele Detection feature, which will currently detect novel SNP’s only.

Additional Notes:

• Novel allele detection mode is known to cause a few ordering issues, where a novel allele may mistakenly get reported as the best match.  An example is HLA-A:01:01:01:01 reported as HLA-A:01:11N#1, which should be reported as ambiguous but isn’t.  Note, this does not affect the ‘Exons Only’ analysis mode, and will be resolved for the other analysis modes in the next release.
• The threshold for novel SNP detection is currently very high, 90%+ of the reads need to have the SNP.

As usual, all feedback and comments are welcome.

Sincerely,

The Omixon Team

Technical Assistance: support@omixon.com

Product Information: sales@omixon.com