Omixon Biocomputing

Budapest, Hungary

Omixon Biocomputing

Budapest, Hungary
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Ruiz-Carmona S.,University of Barcelona | Alvarez-Garcia D.,University of Barcelona | Foloppe N.,Vernalis | Garmendia-Doval A.B.,Amper Programas | And 7 more authors.
PLoS Computational Biology | Year: 2014

Identification of chemical compounds with specific biological activities is an important step in both chemical biology and drug discovery. When the structure of the intended target is available, one approach is to use molecular docking programs to assess the chemical complementarity of small molecules with the target; such calculations provide a qualitative measure of affinity that can be used in virtual screening (VS) to rank order a list of compounds according to their potential to be active. rDock is a molecular docking program developed at Vernalis for high-throughput VS (HTVS) applications. Evolved from RiboDock, the program can be used against proteins and nucleic acids, is designed to be computationally very efficient and allows the user to incorporate additional constraints and information as a bias to guide docking. This article provides an overview of the program structure and features and compares rDock to two reference programs, AutoDock Vina (open source) and Schrödinger's Glide (commercial). In terms of computational speed for VS, rDock is faster than Vina and comparable to Glide. For binding mode prediction, rDock and Vina are superior to Glide. The VS performance of rDock is significantly better than Vina, but inferior to Glide for most systems unless pharmacophore constraints are used; in that case rDock and Glide are of equal performance. The program is released under the Lesser General Public License and is freely available for download, together with the manuals, example files and the complete test sets, at http://www.w3.org/1999/xlink. © 2014 Ruiz-Carmona et al.


Major E.,Omixon Biocomputing | Rigo K.,Omixon Biocomputing | Hague T.,Omixon Biocomputing | Berces A.,Omixon Biocomputing | Juhos S.,Omixon Biocomputing
PLoS ONE | Year: 2013

Specific HLA genotypes are known to be linked to either resistance or susceptibility to certain diseases or sensitivity to certain drugs. In addition, high accuracy HLA typing is crucial for organ and bone marrow transplantation. The most widespread high resolution HLA typing method used to date is Sanger sequencing based typing (SBT), and next generation sequencing (NGS) based HLA typing is just starting to be adopted as a higher throughput, lower cost alternative. By HLA typing the HapMap subset of the public 1000 Genomes paired Illumina data, we demonstrate that HLA-A, B and C typing is possible from exome sequencing samples with higher than 90% accuracy. The older 1000 Genomes whole genome sequencing read sets are less reliable and generally unsuitable for the purpose of HLA typing. We also propose using coverage % (the extent of exons covered) as a quality check (QC) measure to increase reliability. © 2013 Major et al.


PubMed | Omixon Biocomputing
Type: Journal Article | Journal: PloS one | Year: 2013

Specific HLA genotypes are known to be linked to either resistance or susceptibility to certain diseases or sensitivity to certain drugs. In addition, high accuracy HLA typing is crucial for organ and bone marrow transplantation. The most widespread high resolution HLA typing method used to date is Sanger sequencing based typing (SBT), and next generation sequencing (NGS) based HLA typing is just starting to be adopted as a higher throughput, lower cost alternative. By HLA typing the HapMap subset of the public 1000 Genomes paired Illumina data, we demonstrate that HLA-A, B and C typing is possible from exome sequencing samples with higher than 90% accuracy. The older 1000 Genomes whole genome sequencing read sets are less reliable and generally unsuitable for the purpose of HLA typing. We also propose using coverage % (the extent of exons covered) as a quality check (QC) measure to increase reliability.


PubMed | Omixon Biocomputing and Children's Hospital of Philadelphia
Type: Journal Article | Journal: Clinical chemistry | Year: 2016

Routine, high-resolution human leukocyte antigen (HLA) genotyping by next generation sequencing within clinical immunogenetics laboratories can now provide the full-length gene sequence characterization of fully phased HLA alleles. This powerful technique provides insights into HLA variation beyond the traditionally characterized antigen recognition domain, providing sequence annotation across the entire gene including untranslated and intronic regions and may be used to characterize novel alleles from massively parallel sequencing runs.We evaluated the utility of the Omixon Holotype HLA assay to generate credible, fully phased full-length gene consensus sequences for 50 individuals at major histocompatibility complex, class I, A (HLA-A), HLA-B, and HLA-C loci (300 genotyped alleles in total) to identify and characterize novel class I HLA alleles using our downstream analytical pipeline.Our analysis revealed that 7.7% (23/300) of genotyped class I HLA alleles contain novel polymorphisms. Interestingly, all of the novel alleles identified by our analysis were found to harbor sequence variations within intronic regions of the respective locus. In total our analysis identified 17 unique novel class I HLA alleles from 23 of the 300 genotyped alleles and generated full-length gene sequence annotations for 9 previously incompletely annotated HLA class I allele sequences derived from 14 of the 300 genotyped alleles.The demonstrated utility of the Omixon Holotype HLA assay in combination with our downstream analytical framework to generate fully phased, full-length gene consensus sequences for the identification and characterization of novel HLA alleles, facilitates the study of HLA polymorphism beyond the antigen recognition domain in human health and disease.

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