Genotyping By Next Generation Sequencing

In previous blog posts, we talk about the techniques available for genotyping (Genotyping: From qPCR to microarrays and NGS sequencing) as well as the discussion of when to choose microarrays, when next generation sequencing and when to combine both techniques (Microarrays or sequencing? How to choose?). Now we present the genotyping by Illumina sequencing.

Next-generation sequencing, by itself, allows access to the genotype of one or more biological organisms, and in a timely manner, the methods that describe the genetic variation in them are diverse.

The choice of a method for genotyping by sequencing requires knowing what you want to achieve or knowing through experimentation. Here are the 3 most common essays:

  1. On the one hand, genome sequencing and complete exomewhole-genome sequencing / whole-exome sequencing ) enable the discovery of variants associated with complex or polygenic features. Both methods allow genotype-phenotype correlations to be performed as in the GWAS (Genome Wide Association Studies ) studies that have allowed the description of the association of genotypes with rare or complex diseases.
  2. On the other hand, the Genotyping by sequencingGenotyping-By-Sequencing – GBS ) by the method of sequencing targeted ( targeted sequencing ) is the high – performance option most powerful and cost-effective way to discover, validate and detect genes on specific routes and / or for the continuation and monitoring of GWAS studies. This, since it allows focusing on genes and / or genomic regions of interest, which reduces the amount of study information. This type of GBS assays are usually combined with genotyping by microarrays for the characterization of large populations of organisms.
  3. Finally, a large part of the microarray assays are being migrated to applications in transcriptomics by means of RNA-seqof messenger RNA (mRNA) that allows obtaining a broader picture of the genetic expression profile. Due to the resolution power offered by RNA-seq, it becomes possible not only the detection but also the discovery of new transcripts or unknown variants.

In the following tool you can know the directed sequencing panels that are already designed and ready for use

Sequencing Assay Designer

  1. Register an account in DesignStudio (free)
  2. Select Start New Design
  3. Select the type of nucleic acid
  4. Select the technology you would like to explore
  5. Select the species of interest
  6. Name and describe your panel design
  7. Choose the type of sample (regular, FPPE, cfDNA)
  8. Click Next
  9. In the Genetab , add the name or names of the gene or genes of interest
  10. Request the final design – Submit design
  11. Wait for the tool to calculate the coverage parameters
  12. With your design, request an investment proposal


by Abdullah Sam
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