Genotyping or genotyping allows us to explore genetic variants such as single nucleotide polymorphisms and structural changes in DNA. In contrast, high-performance technologies such as microarrays and next-generation sequencing have allowed a deeper understanding of the relationship between genotypes and phenotypes in different biological organisms (associations: genes and complex traits, genes and diseases).
Then, knowing these two characteristics, comes the million dollar question, how to choose between microarrays and sequencing to efficiently develop my study?
In general, the answer lies in the objective of the test you wish to perform.
Because the main difference between both techniques is the resolving power, next generation sequencing allows focusing efforts to discover new genetic variants while microarrays allow solving the detection and monitoring of variants already known and studied.
Currently, microarray-based methods allow analyzing and detecting regions of the genome that may be associated with phenotypic features of interest. However, with the reduction continuous sequencing costs, both techniques and combine in assays also require detecting known variants, new discover variants associated with complex traits such as in assays of genotype-phenotype association ( genome-wide studies ) .
Fig. 1 – A cycle of discovery and detection of variants. Illumina 2019
Thus, if the desired objective is to detect and monitor a known number of variants in a high number of available samples, then the microarrays for genotyping are the most cost-effective technique available. If, on the contrary, what is desired is to interrogate a high number of variants such as SNPs, indels, low-expression or low-frequency transcripts with a high capacity for discovery, next-generation sequencing is the most viable and major option resolving power
Here is a free online tool that allows you to learn about the Illumina kits that are required for sequencing and microarray methods in different applications.
Library Prep and Array Kit Selector
- Select your application area
- Select the application of interest
- Select the sequencing or microarray method
- Select the species of interest (optional)
- Select the sequencing or microarray platform (optional)