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Metagenomics: powerful analyses of microbial communities

Molecular metagenomics is used to analyze a community of organisms as a whole; as such, it provides an exhaustive assessment of a complex ecological niche. It is a powerful, innovative approach for characterizing the genes and thus the biological functions in a given microbiome.

Targeted sequencing - An in-depth analysis of regions of interest

Targeted sequencing allows specific analysis of targeted genes (or gene regions) on many samples in parallel. With NGS sequencing on MiSeq^®, NextSeq500^® or Hiseq^® platforms, multiple genes can be evaluated with a smaller data volume, which is easier to manage and analyse than WGS datas.

Applications

Exome sequencing

This type of sequencing is essentially used to:

• Screen for mutations in genes involved in regulatory pathways
• Screen for mutations (SNPs, indels, etc.) associated with a particular disease (cancer, coagulopathies, etc.).

We use the NimbleGen SeqCap EZ protocol (Roche) for exome sequencing.

Personalized sequencing

After custom probe design, your regions of interest are enriched prior to sequencing which simplifies the subsequent data analysis. This protocol can be set up for any organism with an available reference genome.

GenoScreen's assets

• A dedicated team of scientists for each project.
• Comprehensive support with the elaboration of an experimental plan and project implementation.
• Assistance with data handling and interpretation of the results.

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Ready-to-load services - Plugged into our sequencing platform

For a cost effective and responsive offer, GenoScreen proposes "Ready to Load" sequencing services for a wide range of libraries: a real research accelerator giving the opportunity to perform on last generation technical platform with advanced expertise.

Applications

Transcriptomics - Analyzing gene expression

High-throughput sequencing of the transcriptome (RNA-Seq) has revolutionized the quantitative and qualitative analysis of prokaryotic and eukaryotic organisms.

Whole-genome sequencing - A high-precision method for characterizing the genome

The latest sequencing technologies make it possible to analyze the full primary structure of an isolated organism’s genome, regardless of, whether the latter is a eukaryote, a prokaryote or a virus.
An analysis of whole-genome sequencing data provides a precised description of any type of organism and thus addresses a very broad range of research questions.

Applications

MLST/MLVA, microbial typing/tracing solutions

GenoScreen proposes you the opportunity to characterize more accurately your microorganisms (subspecies or strain characterization) using standardized and validated molecular biology methods such as MLST or MLVA (including MIRU-VNTR).

MultiLocus Sequencing Typing (MLST)

Pricing

The MLST (MultiLocus Sequencing Typing) sequencing typing is the reference technique for the distinction of different strains. This method is based on the house-keeping genes sequencing (house-keeping genes are encoding essential proteins of the bacterium).

These sequences have the particularity of presenting a stable polymorphism over time and sufficient enough to distinguish strains from each other.

This approach allows the characterization of a microorganism whose genus (or species) is known in order to identity the species(or subspecies) and this thanks to the sequencing of 7 house-keeping genes.

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The MLST by GenoScreen

GenoScreen's MLST service offer is a complete package of services realized from extracted DNA or thermolysate. This includes the PCRs realization, the sequencing on a capillary sequencer, the sequences analysis and the strain assignment..

Multiple Loci VNTR Analysis (MLVA)

Pricing

The MLVA (Multiple Loci VNTR Analysis) is a genetic analysis method of VNTR (variable number of tandem repeats) pattern polymorphism based on their count. During a first step, each targeted VNTR locus is amplified by PCR with flanking-region specific primers. The fragments obtained are then separated according to their size by electrophoresis on capillary sequencer. The genotyping of each locus and the results compiled from each sample allow to assign to the strain a specific numerical code for a subspecies.

The MLVA approach allows to characterize a microorganism whose species is known, to identify, at least, the subspecies through allele typing and comparison to the MLVA databases. This method is more selective than the MLST method and does not require a DNA sequencing step. It thus makes it possible to differentiate close subspecies (clonal species).

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Le MLVA par GenoScreen

GenoScreen's MLVA service offer is a complete package of services realized from extracted DNA or thermolysate. This includes the PCRs realization, the electrophoresis on a capillary sequencer, the data analysis and the strain assignment. 

The analysis can be carried out on the basis of a personalised typing scheme tailored to your needs, in line with the data available for your species. 

SNP genotyping

This technique is based on the variation of a single nucleotide at a given position (Single Nucleotide Polymorphisms), which can lead to functional changes in the genes and proteins resulting from the modified amino acid sequence. By offering genome-wide analysis, GenoScreen can help you identify unknown genotype-phenotype associations or genetic variations that are already known.

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In what context should microsatellite genotyping be carried out?

Since SNPs can be found in any type of genome, genotyping them can be of interest in a wide range of applications. Our team is used to working on a wide range of problems, and can help you choose the best technique to meet your needs.

GenoScreen offer

Our services are tailored to your needs. We can use assays already available in databases, or identify and target SNPs of interest from sequencing data (with or without a reference genome).

Genotyping by qPCR

qPCR is used to identify genetic variations such as SNPs by specifically amplifying DNA sequences. This genotyping is based on methods such as TaqMan probes, which offer precise discrimination of alleles, or KASPar competitive PCR, which is more economical for large-scale or recurrent analyses.

These two methods for identifying genetic variants operated by GenoScreen will be proposed to you depending on the purpose and recurrence of your project. Our team can also help you design a genotyping kit.

 

 

A tailored approach to meet your needs

We work with you to plan all the stages required to bring your project to a successful conclusion, whatever your constraints in terms of number of samples or targets, timeframe and cost.

 

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Genotyping by sequencing

 

These technologies are commonly used in population genetics, conservation biology and ecology projects. It is not necessary to have access to a reference genome to carry out the analysis.

The data obtained can be used to identify SNPs as genetic markers, perform population structure and/or phylogenetic analyses.

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Sanger

Thanks to its reliability and accuracy, Sanger sequencing remains the reference method when it comes to verifying uncertain qPCR results or confirming mutations observed by high-throughput sequencing.