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SSR microsatellite genotyping

This technique is based on the amplification of short DNA sequences composed of repeating units of a few nucleotides. Because of their polymorphism, microsatellite markers can be used to study genetic diversity within a species or population. GenoScreen has developed almost 20 years of expertise in the study and analysis of microsatellites, enabling the development of markers for more than 500 species.

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When should microsatellite genotyping be used?

GenoScreen offer

 

 

 

Use of existing data

As microsatellite markers are molecular reference tools, there are many publications and previous works available today that we can draw on to meet your needs. We can also use existing data on closely related species (cross-amplification) or from high-throughput sequencing.

Whenever markers are already available for your species of interest, we can use the amplification conditions developed or develop new ones to, for example, group together markers from different publications or use only some of them. There are several possible scenarios:

Features

Multiplex development

(several pairs of primers)

From previously published publications / markers

Cross-amplification

Custom

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Development of de novo markers

 GenoSat® - GenoScreen offer

Geno Sat^® is a standardised, simple and modular solution for all types of eukaryotic species. Since 2009, our solution has already been used on more than 500 different species as part of phylogenetic studies, biodiversity analyses and conservation programmes. This solution enables :

• Production of microsatellite libraries using high-throughput sequencing,
• Development of polymorphic markers of interest
• Population genotyping

Pricing

Geno Sat®

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Using 1 µg of genomic DNA and Illumina MiSeq high-throughput sequencing technology, GenoSat® can produce bioinformatically validated primer pairs within 2 months, framing the microsatellites identified for your species.

Geno Sat® Pack

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This modular solution lets you both biologically validate a batch of primer pairs (after in silico validation), and study the polymorphism of successfully amplified pairs.

Geno Sat® Pack +

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The Geno Sat® Pack + solution is our most comprehensive offering for optimising multiplexes and/or genotyping large populations using polymorphic microsatellite markers of interest.

Discover the list of species analysed with Geno Sat® below:

 

Fragment analysis

Equipped with ABI 3730XL capillary sequencers, we can respond rapidly to your needs for fragment analysis (microsatellites, SSR, STR, etc.) using your labelled PCR products supplied in 96-well plates.

We offer sliding scale prices depending on the number of plates received per batch and migrated with the same size marker.

It is also possible to send us plates ready to be migrated using the same principle, already containing the Hi-Di Formamide + size marker mix with your sample.

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Identifying and genotyping

The identification and genotyping are essential in the discovery of genetics variations, specially in the studies of the populations and pathologies.

These analyses are extremely informative for many key scientific activities:

• Food traceability.
• Biomarker development and validation (screening/diagnostics, functional genomics, trait prediction models, etc.).
• Studies of genetic diversity and evolution (phylogeny, etc.).
• Identification of individuals (criminals, bodies) or links between individuals (paternity tests).
• Genomic selection (agriculture, animal husbandry, etc.).

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Bioinformatic reports

 

Explore our bioinformatic reports below.

 

Discover our report (de-novo assembly)

 

Discover our report (differential gene expression)

 

Ready-to-publish methodology

 

 

• Detailed material and methods section

• Transparency on the tools used

• References and sources already formatted for publication

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Genome comparisons and mutation detection

One of the biggest challenges in genomics is being able to connect a phenotype to the available genetic information. Mutation detection and whole-genome comparison techniques can go beyond the simple observation of a genome, in order to make an evolution in your researches.

Applications of genome comparison and mutation detection

Whole-genome comparisons and mutation detection are deployed to identify genes and mutations of interest with regard to a molecular or cellular phenotype (antibiotic resistance, enzyme activity, etc.).

These two approaches make it possible to set up new genomic selection criteria in agriculture, identify drug targets, select specific strains, and discover novel biomarkers, for example.

GenoScreen offer - Mutation detection

Mutations of interest (SNPs or indels) are detected by comparing similar sequences (e.g. genomes/transcriptomes from two members of the same species).

This comparison involves mapping the sequences on a reference sequence. The segment of the reference genome covered must be similar for the two compared sequences.

The GenoScreen's assets

• Specific processing of sequencing information in order to improve their quality and clarity.
• Detailed annotation of genes and sequences of interest.
• Precise algorithms for alignment with reference sequences.
• Whole-genome comparisons.

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Bioinformatics - Giving a clear answer to your research questions

GenoScreen develops a broad range of bioinformatics services - notably those designed to help interpret data generated by NGS. Our algorithms provide clear, precise answers to all types of genome-related issues.

Exclusive tools for interpretation and analysis

Our bioinformatics services are permanently powered by the results of our R&D programs. GenoScreen detains tools for post-processing raw sequencing data - guaranteeing the highest possible quality of information.

Many specific algorithms have been developed in collaboration with our genomics experts in order to provide a faster results interpretation and also a better understanding and a denser scientific information.

• De novo assembly and mapping.
• Functional and structural annotation.
• Genome comparison.
• Transcriptome and differential expression analyses.
• Metagenome analysis.

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Differential gene expression - Understanding the impact of genes on cell behavior

Gene expression is a major field of investigation with the goal of a better understanding of the mechanisms of action that underlie a cell’s behavior. GenoScreen offers a comprehensive range of differential genomics analyses, so that you can identify biomarkers of interest.

Applications of differencial genomics

RNA-Seq technologies provide the differential expression analysis of an entire genome in an organism and the comparison of the level of gene expression between two conditions, for the research of biomarkers of interest :

• Comparisons of healthy and diseased tissues.
• Comparisons of cell behavior in two different environments (as a function of nutrition, stress, pollution, etc.)
• Comparisons of cell behavior at different stages of biological development.

This exhaustive approach has several advantages:

• No requirement for prior knowledge of the organism being studied.
• Whole-transcriptome analysis, hypothesis-free on the genes of interest.
• The ability to use sequencing data to generate a transcriptome de novo.
• Analysis of natural antisense transcripts (NATs).

GenoScreen - Differencial genomics services provided

Our teams offer comprehensive and personalized support:

• Assistance with study design
• RNA purification
• Library preparation and sequencing
• Pooling and sequencing
• Bioinformatics analysis

GenoScreen's assets

• Full-service provision from study design to bioinformatics analysis of the results.
• Optimized protocols for maximizing sensitivity, reliability, and reproducibility.
• Precise summary reports, detailing the most significant differences.

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Assembly - The reliable reconstitution of genomic data

The high performance level of NGS technologies is largely based on bioinformatics methods capable of reassembling entire sequences (contigs or scaffolds) from a very large number of fragments of genomes or transcriptomes.

The first task is to organize and assemble these fragments of information on a reference genome. The goal is to identify variants with the standard, then, to understand their roles and impacts (annotation and interpretation). To this end, our bioinformaticians use semi-automated processing algorithms.
This requires considerable calculation and analytical capacities, knowing genomics is now one of the leading consumers of high-performance calculation (HPC) and big data services.

Along with the calculation power, the data storage constitutes another major challenge in terms of volume, performance and security in genomics. In fact, GenoScreen keeps a high level of sensitivity and confidentiality of your data.

Applications - Assembly

The assembly allows the reconstitution of a whole genome using new sequencing techniques, either based on a reference genome or via a de novo approach.

This reconstruction gives a comprehensive, detailed image of genomic data that facilitates the latter’s interpretation.

GenoScreen - Assembly services provided

In order to obtain the best results, GenoScreen combines the most suitable methods for each case :

• De novo assembly, which assembles the reads generated by sequencing (of a genome or transcriptome) into longer sequences (contigs or scaffolds) with the objective of determining the entire sequence of a chromosome or a transcript.
• Mapping which aligns the short fragments on a reference sequence in FASTA format.

Our teams use several algorithms to optimize the length of the assembled contigs and thus reduce the assembly error rate as much as possible.

GenoScreen's assets

A low error rate, credits to our exclusive de novo assembly techniques.

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