With the same focus, #SpecializedDiagnostics, Werfen and Omixon are the perfect match. The Omixon team is excited to join Werfen and contribute to #PoweringPatientCare.
The most widely used file format for reference sequences is the fasta format. Both nucleotide and protein sequences can be represented in fasta format.
A fasta formatted file begins with a single-line description, followed by the sequence data. The description line starts with a greater-than (“>”) symbol. In the next line, the nucleotide or protein sequence starts. This sequence can be in a single line, but usually it’s broken into shorter, uniform length lines. Coding of the sequences follows the IUPAC code.
The Omixon team traveled again to a fantastic conference. This time our team went to Paris for the European Society of Human Genetics conference. The conference started during the afternoon of the 8th June at the huge Amphiteatre of Palais de Congrés with around 3000 geneticists from Europe.
We see amazing potential in using social media channels for spreading the word about next generation sequencing, HLA typing and bioinformatics in general. This is why we have been writing this blog, updating the Facebook and Twitter channels and now we open a new channel on LinkedIn.
A survey of tools for variant analysis of next-generation genome sequencing data. Pabinger et al. 2013
Following last week”s variant caller themed FF post, I will present you a very great article about variant detection and annotation. The paper gives a great review of basically every aspect of NGS based variant detection from a whole NGS analysis workflow and available tools to specific problems (e.g. detection of somatic mutations).
My favourite part is Figure 2, which illustrates perfectly, that there is no perfect variant caller around, even for germline mutations. Each tool finds (and misses) a different set of variants.
Figure 2 from Pabinger et al. 2013: Venn diagrams showing the number of identified variants for tested germline (A), somatic (B), CNV (C) and exome CNV (D) tools. The depicted numbers in (A) and (B) report identified SNPs and INDELs.
Come and join our CEO, Attila Berces online in a presentation and demo of how Omixon Target HLA typing will bring you value during the analysis of NGS data.
Our guest speaker is Dr. Dimitri Monos, University of Pennsylvania and The Children”s Hospital of Philadelphia, who will talk about his experiences with HLA typing protocol development on NGS platform.
Currently, there are 69 on-going clinical trials investigating HLA as a potential biomarker for safety or efficacy. It appears that beside being the most important marker in transplantation, HLA is becoming a more important biomarker for cancer therapeutic development as well. The analytical performance of NGS-based genetic tests highly depends on the bioinformatics software. Although the current false variant rate can be acceptable for research market, it is simply unsuitable for making clinical decisions. Omixon tailors the analysis for the sequencer, amplification method, primer kit, and the characteristics of the gene target itself. This approach results in a robust and highly accurate method to identify genetic variants.
