With the ever increasing throughput in sequencing technology, data analysis remains a challenge for which high-skilled experts are imperative. ProGenTomics can help you if you do not have the necessary in-house expertise or when you want to out-source and speed-up the analysis of your data. We perform, in collaboration with NXTGNT, data analysis starting from raw sequencing reads (filtering, trimming, mapping of reads), data normalization and statistics, visualization, PCA analysis, Gene-set enrichment analysis, Pathway analysis, etc. Feel free to contact us regarding any question.

Strengths of our bioinformatics team

  • expertise in experimental design
  • expertise in analysis and visualization of genomic, epigenomic and transcriptomic datasets and results
    • differential gene (transcript) expression, also on species without a reference genome (by performing a de novo transcriptome assembly)
    • variant calling, annotation and filtering of causal variants
    • de novo genome assembly
    • epigenetic profiling
  • expertise in data mining trough pathway analysis, gene-set enrichment analysis and PCA analysis
  • expertise in custom application data analysis, answering your specific question

Please feel free to contact us for more information.

Tools and scripts

Mendelian, an heuristic filtering tool to identify phenotype-associated genetic variants

Identification of one or several disease causing variant(s) from the large collection of variants present in an individual is often achieved by the sequential use of heuristic filters. The recent development of whole exome sequencing enrichment designs for several non-model species created the need for a species-independent, fast and versatile analysis tool, capable of tackling a wide variety of standard and more complex inheritance models. With this aim, we developed “Mendelian”, an R-package that can be used for heuristic variant filtering.

Download Mendelian R-package at GitHub.

More information:
Broeckx B et al. 2015. An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors. BMC Genomics 16:391. DOI: 10.1186/s12859-015-0822-7

Canine exome

By limiting sequencing to those sequences transcribed as mRNA, whole exome sequencing is a cost-efficient technique often used in disease-association studies. We developed two target enrichment designs based on the recently released annotation of the canine genome: the exome-plus design and the exome-CDS design. The exome-plus design combines the exons of the CanFam 3.1 Ensembl annotation, more recently discovered protein-coding exons and a variety of non-coding RNA regions (microRNAs, long non-coding RNAs and antisense transcripts), leading to a total size of approx. 152 Mb. The exome-CDS was designed as a subset of the exome-plus by omitting all 3' and 5' untranslated regions. This reduced the size of theexome-CDS to approx. 71 Mb.

To test the capturing performance, four exome-plus captures were sequenced on a NextSeq 500 with each capture containing four pre-capture pooled, barcoded samples. At an average sequencing depth of 68.3x, 80% of the regions and well over 90% of the targeted base pairs were completely covered at least 5 times with high reproducibility. Overall, these designs provide flexible solutions for a variety of research questions and are likely to be reliable tools in disease studies.

Download the exome designs from the Roche website.

More information:
Broeckx B et al. 2015. Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes. Scientific Reports 5:12810. DOI: doi: 10.1038/srep12810
Broeckx B et al. 2014. Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1). Scientific Reports 4:5597. DOI: 10.1038/srep05597

MyFLQ - My Forensic Loci Queries

Forensic scientists are currently investigating how to transition from capillary electrophoresis(CE) to massive parallel sequencing (MPS) for analysis of forensic DNA profiles. MPS offers several advantages over CE such as virtually unlimited multiplexy of loci, combining both short tandem repeat (STR) and single nucleotide polymorphism (SNP) loci, small amplicons without constraints of size separation, more discrimination power, deep mixture resolution and sample multiplexing.

MyFLq aims to bridge the gap between both technologies. Current CE DNA databanks only register length of loci. MPS technologies and software need to be backwards compatible with these databanks. With MyFLq you can generate DNA profiles based on MPS FASTQ files, that result in profiles useful for searches in CE DNA databanks.

Visit the MyFLQ website.

More information:
Van Neste C et al. 2014. My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing. FSI: Genetics 9:1-8. DOI: 10.1016/j.fsigen.2013.10.012
Van Neste C et al. 2015. Forensic massively parallel sequencing data analysis tool: Implementation of MyFLq as a standalone web- and Illumina BaseSpace®-application. FSI: Genetics 15:2-7. DOI: 10.1016/j.fsigen.2014.10.006

FLAD - Forensic Loci Allele Database

FLAD is a simple database for forensic alleles, that offers permanent identifiers to any allele sequence. If a sequence is not yet in the database, a simple registration is sufficient to start adding alleles to FLAD.

FLAD does not provide information about the loci a sequence belongs to, or any other type of annotation. FLAD aims to be a simple identifier service, similar to what doi does for publication identifiers, to provide forensic analysis software with permanent identifiers for sequences.

Visit the FLAD database.

More information:
Van Neste C et al. 2016. Forensic Loci Allele Database (FLAD): Automatically generated, permanent identifiers for sequenced forensic alleles. FSI: Genetics 20:e1-e3. DOI: 10.1016/j.fsigen.2015.09.006

About ProGenTomics

ProGenTomics, located in Gent (Belgium), offers a wide range of proteomics and genomics services and support to the academic community and its external customers. We aim to tailor our services to the needs of our collaborators and customers, while giving great support.  

Contact us

ProGenTomics, proteomics & genomics services

  Ghent University, Faculty of Pharmaceutical Sciences

  Ottergemsesteenweg 460, 9000 Gent, Belgium

 

  +32 9 264 83 56