Experts in SNP genotyping

Reduce sequencing costs with a reduced-representation approach

Reduced-representation methods are based on sequencing only a fraction of the genome instead of sequencing the entire genome. These cost-effective approaches allow for the simultaneous genotyping of hundreds of individuals in the same sequencing run and are able to yield up to thousands of SNPs (single-nucleotide polymorphisms) which can be used in a variety of fields such as population genomics.

At AllGenetics we use a new reduced-representation method to prepare genome libraries, called MobiSeq. MobiSeq was developed by Dr. Anders Johannes Hansen's group at the University of Copenhagen. It generates genomic data based on the PCR-enrichment of transposable elements scattered throughout the genome. The way the technique works is by designing a primer at the conserved end of a transposable element and sequencing its flanking region outside the transposable element. Thousands of such flanking regions are sequenced in each individual, allowing for SNP identification and genotyping across all the individuals being studied.

Despite the need for genomic information on the species under study, MobiSeq has proven advantages over other genotyping-by-sequencing methods such as its suitability for low quality and low concentration DNA samples or the possibility of removing duplicate reads.

How we work

SNP genotyping workflow

Step 1: We sequence one individual of the target species in the Illumina HiSeq X platform to obtain 50 gigabases of genomic information that will be used for primer design. Then, we identify a suitable transposable element and design a primer within a conserved region in its 5' or 3' end.

Step 2: We isolate DNA from your samples. We have several optimised DNA isolation protocols, depending on the starting biological material.

Step 3: We prepare the reduced-representation libraries following the MobiSeq protocol.

Step 4: We sequence the libraries in the Illumina HiSeq X platform. Up to hundreds of libraries can be multiplexed in the same sequencing run and enough coverage of the loci under study can still be obtained.

Step 5: We analyse the high-throughput sequencing data to obtain the genotypes of the individuals under study.

For your convenience, we can carry out the entire project or only those steps you require. As a norm, steps 3 and 4 should be ordered jointly. Please contact us for further information and pricing.

What you receive

A report with a summary of the methods followed.

The raw high-throughput sequencing files, which will be delivered through our server.

The results of the bioinformatic analysis including demultiplexing, pre-processing and quality control of the raw data, de novo assembly, removal of duplicate reads, and allele calling.

If you require additional analyses, please let us know and we will do our best to meet your needs.

At no additional cost, our project specialists will be available to you after project delivery and during the editorial process of your scientific articles. We offer up to five 60-min sessions per project, depending on the project size.

What we need

We can start working by using either your tissue samples, or DNA which has already been extracted.

If you are sending tissue samples, please make sure that they have been properly preserved for DNA isolation (ethanol, silica gel, frozen, or another suitable preservation method). If required, we can provide sampling kits and sample collection guidelines to ensure that your samples arrive at our lab in optimal conditions.

If your DNA has already been extracted, we ideally require at least 400 ng of DNA in TE buffer or water at a minimum concentration of 10 ng/μL, and 260/280 and 260/230 absorbance ratios higher than 1.8.

Please note that, depending on the specifics of your project, these requirements may vary. Please contact us for the specific requirements of your project.

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