Veterinary –omics: bio-informatics and statistical data-analysis

With the development of the so-called second generation sequencers, the research and diagnostical infrastructure has expanded tremendously. Where traditional techniques like Sanger sequencing have their merit for the targeted analysis of relatively small parts of the genome, the newer generations (e.g. the Illumina sequencers) make it possible to sequence large parts or even entire genomes at a relatively limited cost. The large amount of data generated by these sequencers pose a challenge however, as they require specific programming and data-analytical skills, often combined with advanced statistical knowledge. Especially for non-model species, an additional difficulty is that they are often not supported by the tools available.

At the Laboratory of Animal Genetics, we have extensive experience with all these aspects, ranging from data analysis, over the development of new molecular techniques for (non-)model species and the development of new software tools.

The following tools have been developed by us:

A short overview of the novel molecular techniques we have developed and validated:

  • Whole exome sequencing of the dog3,4:
    • The exome-1.0
    • The exome-CDS
    • The exome-plus
  • Whole exome sequencing of the honey bee5

These tools have been used successfully to identify variants associated with Varroa resistence in the honeybee5, as well as for the identification of disease-causing mutations associated with neurological diseases in the dog6.

As we invest strongly in the development of novel molecular techniques, we are also experts in developing novel applications. This has led for example to the development of EG-GWAS (the exome-guided genome-wide association studies)7 and tips for proper experimental design of studies applying whole exome sequencing8.

We also provide data-analysis services for a wide range of data, including transcriptomics, genomics and epigenomics. These tools can be used for a variety of research questions, including “what causes this genetic disease?”, the identification of biomarkers and can result in a deeper understanding of molecular pathways. In the research group, we also actively investigate the so-called “personalized/precision” veterinary medicine.

For more information or if you want to collaborate, please contact us at the following mailing address:

  1. Broeckx, B. J. G. et al. An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors. BMC Bioinformatics 16, 391 (2015).
  2. Broeckx, B. J. G., Peelman, L., Saunders, J. H., Deforce, D. & Clement, L. Using variant databases for variant prioritization and to detect erroneous genotype-phenotype associations. BMC Bioinformatics 18, 535 (2017).
  3. Broeckx, B. J. G. et al. Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1). Sci. Rep. 4, 5597 (2014).
  4. Broeckx, B. J. G. et al. Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes. Sci. Rep. 5, 12810 (2015).
  5. Broeckx, B. J. G. et al. Honey bee predisposition of resistance to ubiquitous mite infestations. Sci. Rep. 9, (2019).
  6. Van Poucke, M. et al. Truncating SLC12A6 variants cause different clinical phenotypes in humans and dogs. Eur. J. Hum. Genet. 27, (2019).
  7. Broeckx, B. J. G. et al. An exome sequencing based approach for genome-wide association studies in the dog. Sci. Rep. 7, 15680 (2017).
  8. Broeckx, B. J. G. et al. Toward the most ideal case-control design with related and unrelated dogs in whole-exome sequencing studies. Anim. Genet. 47, 200–207 (2016).