Sequencing
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
Sequencing or targeted resequencing can achieve very specific objectives:
- Screening of genomic regions of interest.
- Complete coverage of coding regions, with a limited volume of genomic data.
- Analysis of microbial genes.
GenoScreen - Services provided
Amplicon sequencing
A number of the target regions are amplified by PCR, using the initially defined specific primers. The amplicons obtained are then sequenced by NGS, following the addition of sequencing adaptors. Multiplexing approaches enable us to sequence several amplicons from different samples in parallel.
The Metabiote® solution
Metabiote® is a dedicated, innovative, optimized, standardized solution developed by GenoScreen. It integrates targeted metagenomic analysis of microbial communities.
- A library preparation methodology that limits between-sample bias.
- A diverse range of targets:
• bacterial targets: 16S rDNA
• fungal targets: 18S, ITS1 and/or ITS2 rDNA - A bioinformatics pipeline that has been optimized and automated for high-precision analyses, easy comparisons and statistical analyses, and a high degree of responsiveness.
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.
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
"Ready-to-load" applications are available for mainly all of GenoScreen’s sequencing services:
- De novo sequencing or re-sequencing.
- RNA-Seq.
- Targeted sequencing.
- Metagenomics.
GenoScreen - Services provided
"Ready-to-load" sequencing is performed on latest-generation technical facilities: Illumina HiSeq®2500, MiSeq®, NextSeq®500 and HiSeq®4000 systems in paired-end or single-end runs of 50 to 250 bp.
GenoScreen performs quality control on the libraries with bioAnalyzer and fluorimetric assays. GenoScreen can also ensure the pooling of the sequencing libraries, if required.
We accept different types of librairies:
- TruSeq.
- Nextera(-XT).
- Amplicons.
- RADseq or ddRADseq with index and Illumina adaptors.
For the other types of librairies, please contact us.
The results
- Raw sequences (FastQ files) and quality control results after demultiplexing.
- Quality reports, including the number of reads obtained, the number of reads after application of quality filters, and the coverage obtained.
- The results are transferred to a secure FTP server or an external hard disk.
GenoScreen's assets
- Cutting-edge technical facilities.
- A top-of-the-range service at a keen price.
- Responsiveness.
Transcriptomics - Analyzing gene expression
High-throughput sequencing of the transcriptome (RNA-Seq) has revolutionized the quantitative and qualitative analysis of prokaryotic and eukaryotic organisms.
RNA-Seq significatively enables differential expression analyses:
- Measurement of the relative abundance of transcripts.
- Identification of the genes expressed differentially in various groups (tissues, treatments, etc.)
Applications
Transcriptome sequencing provides a complete, objective analysis of messenger RNAs:
- Differential expression: assessment of variations in the expression of several transcriptomes.
- Annotation of a transcriptome against a reference database.
- Identification of all specific sequences of the studied transcriptome.
- SNP analysis.
GenoScreen - Services provided
Two methods are used to enrich the RNA fraction of interest (mRNA) prior to cDNA synthesis and library preparation:
- Poly(A) capture (for eukaryotic total RNA).
- RNA depletion (via capture with complementary probes) and mRNA enrichment (for prokaryotic or eukaryotic total RNA).
Most of our RNA-Seq libraries are sequenced on Illumina® HiSeq®4000 systems.
GenoScreen's assets
- A dedicated team of scientists for each project.
- Assistance with elaborating the experimental plan and sequencing strategy.
- RNA extraction, quantification, purification, and quality control.
- Assistance with data management and interpretation of the results.
- Analysis of differential expression in the absence of a reference genome.
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
Whole-genome sequencing addresses important research questions in many sectors (healthcare, nutrition, agrifood, environment, etc.):
- Description of an organism’s genes and how they are organized.
- Quantification of diagnostic or phenotypic biomarkers.
- Screening for susceptibility/adaptability/resistance genes.
GenoScreen - Services provided
As specialists in whole-genome sequencing (WGS), our expert teams are able to build you a custom solution.
Our precise, fast solutions combine NGS and Sanger techniques and are implemented in cutting-edge technical facilities.
Our bioinformatics solutions can, then deliver in-depth processing and analysis of your WGS data (assembly, annotation, etc.).
- Genome structure and mapping of isolated organisms.
- Comparative genomics: identification of SNPs, indels and/or major structural rearrangements.
- Multilocus sequence typing (MLST).
GenoScreen's assets
- We understand your needs and provide personalized support.
- Exclusive bioinformatics analyses.
- Significant expertise in sequencing microorganisms (bacteria, fungi, yeasts, algae, etc.).
- Fast solution.
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