Genomics - PGEN

Equipment

• Illumina MiSeq sequencer for targeted NGS
• Applied Biosystems SeqStudio for Sanger sequencing and sample/cell-line authentication
• Affymetrix GCS3000 scanner (for e.g. molecular karyotyping with Cytoscan 750K Arrays)
• Agilent Tape Station for sample quality assessment (RIN, DIN) and quantification
• HPC cluster for bioinformatics processing of NGS data (WES, WGS, panels, RNASeq)

Offered service

Sequencing

• Advice for exome [WES], genome [WGS], targeted panels and transcriptome [RNAseq] sequencing (experimental design, sample preparation, QC interpretation).
• Sequencing using PGEN equipment (see above).
• Outsourcing sequencing in accordance with public procurement regulations.
• Contact us for pricing information.

Bioinformatics

Massive parallel sequencing analysis

Most NGS technologies generate data in the form of reads, gathered in a file (e.g. FASTQ for Illumina technology). These “raw” data are useless until they are processed by different algorithms to generate “analyzable” data (e.g. variant calls from exome sequences). We call this process “tier-1 analysis” and it consists of a pipeline of software that performs multiple treatments on the raw data. For example, if you have performed a genome, exome or gene panel sequencing, you will have one or more FASTQ files as raw data. A typical tier-1 pipeline will align the reads to a reference genome, clean the resulting alignment (e.g. by removal of duplicated reads, local realignment, base scores recalibration) and call variants. The resulting files will include an alignment (BAM file) and a variant call (VCF file), that can be further analyzed by users.

Available services

The PGEN platform offers technical and scientific support for any project involving sequencing. We analyze exomes [WES], genomes [WGS], gene panels [panels] and transcriptomes [RNAseq]. The platform proposes bioinformatics support for NGS analyses including the following services:

• Tier-1 analysis of raw NGS data through our pipeline (e.g. alignment, clean of the data and variant calling on genome/exome/panel data, generating BAM and VCF files from a FASTQ).
• Tier-2 analysis of NGS data, through our in-house software Highlander.
• Consultancy : for scientific projects with specificities not covered by the standard and Highlander pipelines, the platform offers a consultancy service either in the form of scientific collaboration or for a fee. This also includes occasional supports such as for example :
  • Data transfer (download of external data to the cluster, upload of internal data to public repository, ...)
  • Data quality checking
  • Training (e.g. use of Highlander)
  • Custom data analysis
  • …

All analyses are performed on our cluster by our bioinformatician (see contact below), but personal cluster access can also be granted. Please contact us for any collaboration.

Pricing

Note that when a service is offered to a UCLouvain external, the 25% PAFG is included in the price which is indicated excluding VAT.

NGS Analyzes

This service includes data management (download/upload of raw data to the cluster as well as their long-term storage), tier-1 analysis via the appropriate pipeline (generating BAM, VCF and QC), import into the Highlander database, and unlimited access to the software for tier-2 type analyzes by the applicant himself.

For this service, we offer a rate per sample proportional to the service provided.

Note that consultancy fees (see below) may be added in the event that your data requires an adjustment to the pipeline, and the latter only benefits you (e.g. setting up a specific reference genome).

RNAseq (basic) analyzes only include the tier-1 pipeline: alignment, quantification, SNV, INDEL, SV (fusion, LINE) variant calling and import into Highlander, but no other tier-2 analyzes such as differential expression.

If you want differential gene expression and alternative splicing analysis, add the "RNAseq DGE" fee per comparison to the fee per sample.

"Target CRISPR seq" is a unique fee for micro-panels on very few genes to check for CRISPR induced mutations, independently of the number of samples.

Consultancy

The consultancy service for scientific projects can be provided in the form of collaboration or priced as follows (to be defined with the platform manager during the analysis of the project).

The pricing varies according to which profile will be involved in the project: bioinformatician, computer developer or a "mix" of the two.

If the time to invest on the project is short and predictable, we operate with hourly billing.

If the total time to be invested in the project is difficult to predict and/or will be fragmented over time, we offer different short, medium or long packages which correspond approximately to 1 day, 2-3 days or an “aggregate” week of work.

Pricing for larger projects will be defined during its analysis.

Highlander

Since NGS produces tremendous amounts of data, variant call analyses are not trivial. For this “tier-2 analysis”, bioinformatics support is generally essential, but most tools are too complex for use by non-informaticians. For this reason, we developed Highlander, which allows biologists to analyze their NGS data via a user-friendly graphical interface. Please check the project home page for further information.

Training in genomic data analysis

Before working with NGS data and/or Highlander, we strongly suggest you to watch the following training videos.

Theorical seminar on genomic NGS data generation and analysis

• Part 1 - Introduction to NGS
• Part 2 - Alignment
• Part 3 - Variants calling
• Part 4 - Structural variants calling
• Part 5 - Somatic variants calling
• Part 6 - Variants annotation
• Part 7 - Variant effect prediction
• Part 8 - Quality control

Training on usage of Highlander software

• Part 1 - Databases
• Part 2 - Basic filters
• Part 3 - Advanced filters
• Part 4 - Customization
• Part 5 - Alignments and user annotations
• Part 6 - Allele frequencies and effect prediction
• Part 7 - Other annotations
• Part 8 - User profile
• Part 9 - Tools

If you prefer, you can watch similar training seminars recorded in french.

Séminaire théorique sur la génération et l'analyse des données génomiques NGS

• Partie 1 - Introduction au NGS
• Partie 2 - Alignement
• Partie 3 - Appel des variants
• Partie 4 - Appel des variants structurels
• Partie 5 - Appel des variants somatiques
• Partie 6 - Annotation des variants
• Partie 7 - Prédiction de l'effet des variants
• Partie 8 - Contrôle qualité

Formation sur l'utilisation du logiciel Highlander

• Partie 1 - Bases de données
• Partie 2 - Filtres simples
• Partie 3 - Filtres avancés
• Partie 4 - Profil et personnalisation
• Partie 5 - Outils
• Partie 6 - Description des annotations

You can also download the full videos if you prefer (do not watch them directly in Dropbox on your web browser, they seems to be limited at 2 hours max, but are longer).

• English version
  • Theorical seminar on genomic NGS data generation and analysis
  • Training on usage of Highlander software
• French version
  • Séminaire théorique sur la génération et l'analyse des données génomiques NGS
  • Formation sur l'utilisation du logiciel Highlander