Experts in SNP genotyping
Get to know our SNP genotyping service
AllGenetics' SNP genotyping service takes advantage of the new genotyping-by-sequencing method 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. For example, MobiSeq:
- Is species-specific, so DNA from symbiont species will not interfere in the SNP genotyping process.
- Is suitable for low quality and low concentration DNA samples.
Step 1: We sequence one individual of the target species in the Illumina HiSeq or NovaSeq platforms to obtain 90 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 or NovaSeq platforms. 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.
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 analyses including demultiplexing, pre-processing and quality control of the raw data, removal of duplicate reads, de novo or reference-guided assembly, and the results of the allele calling in various file formats (VCF, phylip, and GENEPOP).
If you require additional analyses, please let us know and we will do our best to meet your needs. For instance, we can obtain population statistics as Fst, Fis, expected and observed homozygosis, and heterozygosis.
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.