Genotyping: What is it and why is it important?

Written by: Nermin Đuzić, M.Sc. in Genetics, Content Specialist

Last time we talked about quality evaluation, storage, and management of DNA samples after extraction. These are important steps necessary to ensure the proper DNA yield for further DNA applications. At BioCertica, currently, the main DNA technology being used is genotyping. But before we proceed with genotyping, samples must be prepared for that process.

Our next aim is to explain the basic steps of preparing samples for genotyping and how we perform it. But wait! You may ask yourself, what is genotyping? To illustrate this, let us briefly recall SNPs (single nucleotide polymorphisms). 

SNPs are single-nucleotide changes in DNA sequence, occurring at a specific place in the genome—for example, imagine an SNP at a particular position with two possible variations: C or A nucleotide. Genotyping may reveal that the majority of the population carries the C nucleotide. At the same time, a minority of them have it replaced by A. If you want to learn more about SNPs, you can read our article about genetic variations.

SNP detection

There are two directions in which SNP detection can go: SNP discovery and SNP screening. SNP discovery is a process of discovering new SNPs that are not known yet. Scientists are doing genome-wide scale analysis and discovery of new SNPs in targeted areas. On the other side, SNP screening involves analyzing known SNPs in your genome and determining if they correlate with certain traits or conditions [1]. 

Over the years, many different methods have been designed and developed for the purposes of discovery and screening of SNPs and other genetic variations. Everything started with DNA microarrays and developed to modern and sophisticated methods using even the fluorescence-based approach. Nowadays, the most common and prevalent are medium and high-throughput screening approaches such as:

• SNP microarrays (Affymetrix and Illumina)
• TaqMan SNP genotyping
• MassARRAY SNP genotyping
• SNP genotyping by high-throughput sequencing. [2]

In one of the following articles, we will briefly cover the most common SNP genotyping technologies used worldwide, how they compare and how they developed and have been employed historically. 

What is genotyping and why is it important?

Genotyping is a technique used to detect slight genetic differences characteristic for one person, making them different. In other words, genotyping detect minor genetic variations, such as SNPs among others, that can lead to significant changes in physical appearance, including both traits that make us unique and pathological changes that may cause diseases. Genotyping compares the DNA sequence of our sample of interest to a reference sequence or database with genotype data from a large number of individuals.

You may ask why SNP genotyping is so important? SNPs are the most common genetic variation in humans, appearing approximately at every 1000 nucleotides. It is estimated that an individual has 4-5 million SNPs in the genome [3, 4]. 

They are associated with the determination of traits like eye color or inherited diseases like cystic fibrosis. Also, they may act as markers for the risk of developing complex conditions like diabetes and stroke.

Therefore, SNP genotyping is important as it accelerates the personalized medicine approaches by predicting individuals’ risk of developing common diseases. Also, they may help determine individual-based target therapy in pharmacogenomics.

SNP genotyping applications

After being introduced to the importance of SNPs genotyping, you may ask yourself where it may be useful and applicable. Well, let’s mention some widely-used and well-known applications of that technology.

Disease screening

SNPs are screened for their potential correlation with a particular disease. Here we have to mention genome-wide association studies (GWAS) briefly. GWAS is a research approach in genetics that looks for associations between specific genetic variations and diseases. It includes screening the genetic makeup of many different individuals or even populations and looking for unique genetic markers to predict the chance of getting affected by a particular disease [5].

GWAS may be helpful not only in the identification of risk factors and genetic variants but also for unraveling the biological processes that underlie diseases by identifying potential causes.

Microbiology

SNPs are not only characteristic for humans, but also single-celled microorganisms like bacteria possess SNPs. Screening of bacterial SNPs helps scientists distinguish between different bacterial isolates, essential to characterize antibiotic resistance. This is relevant in agricultural and clinical settings and may be helpful in the detection and study of infectious diseases in plants and humans.

Ecology and Environment 

SNP screening helps us to understand the genetic mechanisms controlling responses of organisms to their natural environments and this helps us with the protection of endangered species and for better management of the natural environment.

At BioCertica, we use Affymetrix Axiom genotyping technology, which is a cost-effective approach that enables complete automation of sample preparation and other steps. In our next article, we will cover the whole genotyping procedure we employ to analyze your DNA. Stay tuned!

References

1. Kwok, P. Y., & Chen, X. (2003). Detection of single nucleotide polymorphisms. Current issues in molecular biology, 5(2), 43-60.
2. Perkel, J. (2008). SNP genotyping: six technologies that keyed a revolution. Nature Methods, 5(5), 447-453.
3. Colbert, R. A. & Glass, D. N. (2005).Chapter 4: INTEGRATIVE GENOMICS. Textbook of Pediatric Rheumatology (Fifth Edition). Pages 64-75
4. Via, M., Gignoux, C., & Burchard, E. G. (2010). The 1000 Genomes Project: new opportunities for research and social challenges. Genome medicine, 2(1), 1-3.
5. National Health Genomic Research Institute. (n.d.). Genome-Wide Association Studies (GWAS). Retrieved from Genome Wide Association Study