Genomic information at the service of human health and its environment
Sequencing
Primer walking
This sequencing method is ideal for:
Principle
The use of several primers makes it possible to obtain overlapping sequences leading to the reconstitution of the complete product. A universal primer is used to sequence an insert, obtaining a fragment of the vector sequence and the beginning of the insert.
A specific primer can then be designed on the sequence obtained and used to obtain the rest of the sequence. If the sequence of interest is known, all the sequencing reactions can be carried out simultaneously. This service can be performed either in single or double reading.
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Mutation detection
Sanger sequencing can be adopted to verify
Principle
Among other applications, the mutation detection is used to monitor TILLING (Targeting Induced Local Lesions in Genomes) in plants, or to verify mutations in genes of interest.
We can design specific primers to target a mutation and compare it to a reference sequence provided for verification.
If several mutations/positions are to be verified in the same genome region, we can also produce a detailed variance report compared with a reference gene.
Molecular barcoding (DNA barcoding) is a molecular taxonomy technique used to identify and genetically characterise a sample from a ubiquitous gene, generally belonging to the ribosomal, mitochondrial or chloroplast genome (COI, 16S, rbcL, etc.).
DNA barcoding applications
DNA barcoding can be used to:
- Identify species from an isolated sample
- Compare several samples from the same species or closely related species (phylogeny)
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Identification by DNA barcoding
GenoScreen offers a complete molecular barcoding service and can handle your samples from DNA extraction onwards.
- Identification of isolated micro-organisms
- Identification of animal or plant species
For complex inital matrices (e.g. assemblies of bacterial populations), GenoScreen develops metabarcoding solutions using NGS amplicon sequencing to obtain screenings of samples: soil fauna, intestinal flora, coral reefs, etc.
GenoScreen offers you a straight-forward service for identifying your micro-organisms by DNA sequencing and comparison with international databases (NCBI or other).
For species identification, the ribosomal DNA regions are adapted to your micro-organism. In addition, other genomic targets (rpoB, gyrB, panC, etc.) can be used to refine this identification and adapt it to your requirements (for example, discrimination within a group of species sharing the same ribosomal DNA sequence).
Identification services
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Workflow applied to isolated microorganisms
Samples extraction
from isolated colonies
PCR amplification on the appropriate genomic target
16S, 18S, 28S, ITS, ...
Forward/reverse sequencing
Purification and assembly
consensus, then comparison
Assignment
Your samples can be extracted on :
- Agar (Petri dishes),
- Liquid culture plates,
- FTA card or other matrix.
PCR amplification on the various targets (16S, 18S, 28S, ITS, etc.) can be carried out using extracted DNA or thermolysate.
We will compare your purified and assembled sequences with the international NCBI database.
Once the assignment has been completed, you will receive:
- Raw sequences and chromatograms (.seq/.ab1)
- Consensus sequences (.txt/.FA)
- Analysis report with homology percentages and assignments per sample.
Complementary solutions
In addition to the identification, we can also generate phylogenetic trees according to your needs (comparison of samples with each other or with a panel of reference sequences).
Depending on your needs, we can also suggest other targets that are more specific to a particular genus, particularly for species that are too close genetically to the default target (e.g. the genus Bacillus with the panC target).
GenoScreen also offers:
- MLST typing, for strains whose species is known and for which a typing scheme is available
- Whole Genome Sequencing (WGS) for more precise characterisation of your microorganisms.
GenoScreen offers you a straight-forward species identification service using DNA sequencing and comparison with international databases (NCBI and/or BOLD).
For species identification, we use target genes from the mitochondrial or chloroplast genome (COI, 16S, CYTB, rbcL, matK, etc.). We have universal primer pairs but we can also adapt to your project, using primers that are more specific to a genus or family depending on the literature.
Other target genes can be used to refine an identification or carry out a more complete phylogenetic study.
In addition to the identification, we are also able to produce phylogenetic trees according to your needs (comparison of samples with each other or with a panel of reference sequences).
Matrices for animal and plant studies
Whole insects or legs/heads
Hairs/feathers
Extracted DNA
Dried or fresh leaves
Blood
Swabs/FTA cards
Tissues (muscle,
organ, fin)
We can work with a wide range of matrices/samples, both invasive and non-invasive:
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Workflow applied to animals and plants
PCR amplification on the appropriate genomic target
COI, 16S, CYTB, rbcL, matK, ...
Forward/
reverse sequencing
reverse sequencing
Purification and assembly
consensus, then comparison
Assignment
We will compare your cleaned and assembled sequences with the international NCBI (or Bold) database.
Once the assignment has been completed, you will receive :
- Raw sequences and chromatograms (.seq/.ab1)
- Consensus sequences (.txt/.FA)
- Analysis report with homology percentages and assignment per sample.
Complementary solutions
In addition to the identification, we can also generate phylogenetic trees according to your needs (comparison of samples with each other or with a panel of reference sequences).
GenoScreen also offers whole genome sequencing (WGS) for a more precise characterisation of your species.
GenoScreen is a major international player providing sequencing and genomic analysis services.
The company’s expertise is based on an unique experience in genomic analyses, the use of cutting-edge technologies and the development and supply of exclusive bioinformatics tools and R&D services. GenoScreen offers a very broad range of sequencing services, from the most basic to the most advanced.
Sanger sequencing
GenoScreen Sanger sequencing services can be adapted to any type of project: magnitudes, delays and production frequencies, for a reading between 100 and 1200 bp.
Next-generation sequencing
GenoScreen offers a complete range of Next Generation Sequencing (NGS) services updated with the latest technologies (Illumina, PacBio ...).
Since 2008, GenoScreen offers a full range of next-generation sequencing (NGS) services in application to genomes, metagenomes and transcriptomes.
GenoScreen has cutting-edge technical facilities, giving you access to the latest technologies (Illumina, PacBio, etc.).
GenoScreen - Services provided
- Whole-genome sequencing (WGS)
New sequencing technologies available at GenoScreen offer the opportunity to analyse the entire primary structure of an isolated organism genome, whether eukaryotic, prokaryotic or viral. The analysis of data obtained allows to precisely characterize and describe any type of organisation and thus responds to a large panel of research problems. - Metagenomics
Metagenomics molecular approaches allows to analyse a community of organisms as a whole and to study a complex ecological niche exhaustively: a powerful and innovative approach to characterize the genes and, therefore, the biological functions carried by these microbiomes. - Targeted sequencing
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. - Transcriptomics
High-throughput transcriptome sequencing (RNA-seq) has revolutionised prokaryotic and eukaryotic organisms quantitative and qualitative analyses. It allows, in particular, to perform differential expression analyses. - Ready to load
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.
The GenoScreen's assets
- A full range of NGS services
- Expert analysis and advice on the design of each analysis
- Unique expertise in microbiology
- High-quality data
- Exclusive bioinformatics tools: assembly, annotation, SNP detection, etc.
- Guaranteed short delay time
Sanger sequencing is a well-proven, low-throughput analytical solution that is well suited to fragments of all sizes (100-1200 bp read length).
GenoScreen’s Sanger sequencing services can be adapted to suit all types of project, regardless the size, delay time or frequency.
GenoScreen - Services provided
Our responsive teams perform the sequencing from the preparation of your samples until the analysis of your data.
Premium Service: a range tailored to your needs
Take full advantage of our expertise!
The Premium range corresponds to the full, personalized analysis of your samples:
- Purification of PCR products as a free option
- Fluorimetric assay
- Protocol adapted to AT or GC-rich sequences if necessary
- A read length of up to 1200 bp
- Shipping within 24 hours
- Technical support by email/phone
The Premium range gives you access to our hotline: expert scientific support for the analysis of sequence profiles.
| One-Shot | One-Shot Plus | Optimized | |
| Results within 24 to 48 hours after receipt | x | x | x |
| Technical support by email and/or phone | x | x | x |
Accepted sample formats:
|
x | x | x |
| Free sample purification (on request) | x | x | x |
| Reading up to 1200 bp | x | x | x |
| Sequence review and corrections with IUPAC annotations | Semi-automated | Manual | |
| Deliverables | .seq / .ab1 | .seq / .ab1 | .seq / .ab1 QC (Quality control) report with comments for each sequence |
| Reprocessing with optimized protocol (on request) | x | ||
| Monthly activity report (including remaining credits) | x | x | x |
The One-Shot Plus offer gives you the benefit of automated enhancement of your sequences using dedicated software. The One-Shot Plus offer includes :
- Signal optimization,
- Background noise reduction,
- Assignment of indeterminate bases.
The Optimized package gives you access to the QC report and manual proofreading/correction with playback commentary for each sequence.
Economic rangge: handle a portion of the task to benefit from lower fees
GenoScreen's quality and responsiveness to assist you.
| Mix & Run | Run Only |
|---|---|
| You provide the DNA/primer reaction mixture in microplates | |
| Sequencing (BigDye® Terminator) | You perform the sequencing reactions and supply the microplates |
| Clean-up of the sequencing products for gel migration | Clean-up of the sequencing products for gel migration |
| Migration on an ABI 3730 xl system | Migration on ABI 3730 xl system |
Additional analyses
Further on, GenoScreen offers additional services to complement the sequencing steps:
- Primer walking for longer fragments,
- Purification of PCR products by gel cutting,
- Primer design and synthesis,
- Verification of PCR products on QIAxcel prior to sequencing,
- Analysis of results according to IUPAC codes.
GenoScreen's assets
- Flexible sequencing services that meet your needs
- Personalized project monitoring
- An easy-to-use ordering system
- Monthly invoicing or a prepaid customer account
- Free sample shipping by a GenoScreen-approved courier
- Optimized sample protection in a Genobox.
GenoScreen advantages
Do you have any questions about administrative procedures or sample shipping and packaging? Find out more about our Sanger sequencing services in our User Guide or by contacting us below:
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Why choose GenoScreen for your sequencing needs?
- Support right from the formulation of your requirements, to find the technique that best suits your needs
- Access to our hotline, expert scientific support for profile analysis
- A flexible sequencing offer that adapts to your needs
- Personalized follow-up of your projects
- Simple ordering system
- Monthly billing or prepaid account
Documentation
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.
In contrast to targeted (profiling) approaches that examine specific, short regions of ribosomal genes, metagenomics is based on the full sequencing of the DNA extracted from a sample (shotgun sequencing).
Metagenomics requires a huge sequencing coverage per sample. This is a limitation for studies of large cohorts, but it provides valuable additional information when profiling a representative subgroup.
Metagenomics has many advantages:
- Removal of the bias associated with PCR approaches
- Culture-free analysis and direct sequencing of microorganisms
- The functional description of a whole ecosystem
Applications
Metagenomics provides an exhaustive analysis of the taxonomic composition of a community of organisms. It provides precise information on the community’s diversity and specific genetic characteristics.
In credit to this direct genetic analysis of microbial communities, metagenomics can also be used to identify new enzymes (biocatalysts) for pharmaceutical, agricultural, industrial and environmental applications.
Metagenomics and human health
Metagenomics is a very well suited solution in diagnosis, evaluation of antibiotic resistance and virus detection, amongst other topics.
It delivers precised solutions in oncology, gastroenterology, dermatology, urology and pulmonology.
Metagenomics and the environment
In credit to its very detailed analysis of microbial communities present in the natural environment, metagenomics can be applied to the analysis of water quality, the development of biofuels and agrochemical products, soil remediation and the development of new practices in agriculture and animal husbandry.
GenoScreen - Services provided
GenoScreen’s standardized methods for metagenomic analysis are able to address all the different aspects of your project. By combining low-, medium- and/or high-coverage sequencing with library preparation (with or without a PCR step), we can offer the solution that best meets your needs.
GenoScreen guarantees the quality of its data produced and uses its exclusive WHORMSS® software to generate a detailed set of results.
GenoScreen's assets
- A dedicated team of expert scientists for each project.
- Assistance with developing the experimental plan and the sequencing strategy.
- Massive whole metagenome sequencing capacity.
- Exclusive bioinformatics tools.
- Cutting-edge scientific expertise for data exploitation (specially in the field of microbiology).
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.
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