What is Genotyping?

Genotyping, an indispensable tool in modern genetics, offers insights into an individual's genetic makeup. This process involves identifying genetic variations within an organism's genome, providing crucial information for various fields, including medicine, agriculture, and research.

Single Nucleotide Polymorphisms (SNPs)

One of the fundamental elements of genotyping is single nucleotide polymorphisms (SNPs), which are variations in a single nucleotide base within the DNA sequence. These SNPs serve as genetic markers and play a vital role in understanding genetic diversity and disease susceptibility.

Single nucleotide polymorphisms (SNPs) are variations in a single nucleotide base within the genome, encompassing substitutions, insertions, deletions, and forming genetic markers. While theoretically, each SNP locus could have four different variants, in practice, only two types occur: transitions and transversions, in a ratio of 2:1. SNPs most frequently appear in CG sequences, with C often converting to T due to methylation-induced deamination of cytosine to thymine.

SNPs are generally considered to have a variation frequency greater than 1%. In the human genome, approximately every 1000 bases harbor one SNP, totaling around 3 million SNPs in the human genome. Consequently, SNPs serve as the third-generation genetic markers, potentially associated with various phenotypic differences, drug responses, or disease susceptibilities.

SNPs, depending on their location within genes, can be categorized into coding regions, non-coding regions, and intergenic regions. While synonymous SNPs in coding regions do not alter protein sequences, non-synonymous SNPs result in amino acid sequence changes. SNPs outside protein-coding regions can still influence gene expression, affecting processes such as splicing, transcription factor binding, mRNA degradation, or non-coding RNA sequences, leading to expression single nucleotide polymorphisms (ESNPs).

CD Genomics high-throughput sequencing and long-read sequencing platforms facilitate the robust analysis of genotyping. This advanced sequencing approach allows for detecting common and rare single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and other genetic variations, providing valuable insights into disease related genetics, individualized health management, breeding, etc.

Insertions and Deletions

Apart from SNPs, genotyping also involves detecting insertions and deletions (INDELs) in the genome. INDELs are variations where nucleotide bases are either added or removed from the DNA sequence, contributing to genetic diversity and disease phenotypes.

What is Genotyping Used For?

Genotyping finds applications in various fields:

  • Clinical Research: It plays a pivotal role in identifying genetic predispositions to diseases, unraveling population genetics intricacies, and crafting targeted therapies. For instance, in HLA typing, genotyping assays offer heightened sensitivity and accuracy over traditional methods, enabling the detection of a broader array of subtypes.
  • Clinical Diagnostics: Genotyping is indispensable for diagnosing genetic disorders, prognosticating disease risks, and tailoring treatment plans for individual patients, thereby ushering in a new era of personalized medicine.
  • Agriculture: Within agriculture, genotyping assumes critical significance for breeding programs, crop enhancement initiatives, and comprehending plant genetics. By integrating genomic variation data with phenotypic information, scientists are paving the way for precision breeding and molecular design strategies. This integration facilitates more precise genetic predictions pertaining to traits such as quality, yield, and stress tolerance, ultimately leading to the development of resilient, high-yielding crop varieties.

How Different Genotyping Methods Work?

  • Genotyping by PCR

Polymerase Chain Reaction (PCR) is a widely used technique that amplifies specific DNA sequences, allowing for the detection of SNPs, INDELs, and other genetic variations.

KASP (Kompetitive Allele-Specific PCR) enables the precise determination of double alleles for SNPs and InDels at targeted loci across diverse genomic DNA samples.

In the realm of SNP genotyping, KASP technology has swiftly dominated the market owing to its exceptional flexibility, accuracy, and cost-effectiveness since its inception. It has emerged as a pivotal auxiliary tool for identifying germplasm resources, conducting population analyses, and facilitating various research endeavors.

  • DNA Microarrays

Microarrays enable high-throughput genotyping by detecting genetic variations across thousands of DNA sequences simultaneously.

DNA microarrays are novel DNA sequence variation detection tools. They exploit the specific hybridization of target DNA with densely arrayed oligonucleotide probes on solid supports to identify SNP alleles.

Advantages: High throughput and versatility, accommodating various genotyping purposes and sample sizes.

Disadvantages: Dependent on the choice of microarray platform and associated costs.

  • TaqMan Fluorescent Probe Method

TaqMan technology, developed by ABI, is a SNP genotyping technique. During PCR, two probes labeled with different fluorophores specifically bind to different alleles. As DNA polymerase extends, the reporter fluorophore is cleaved, emitting fluorescence. SNP genotypes are determined based on the fluorescence signals detected.

Advantages: Simple operation, high accuracy, and ease of interpretation.

Disadvantages: Time-consuming probe synthesis, typically outsourced to ABI.

  • MassARRAY SNP Genotyping

Employing mass spectrometry, this technique precisely identifies single nucleotide polymorphism (SNP) variations within the genome. MassARRAY genotyping utilizes MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight) mass spectrometry, which scrutinizes individual bases based on their mass. The principle underlying this analysis is the detection of base variations at specific SNP sites by discerning the mass disparity of individual bases. The detectable mass range spans about 4500 to 9000 Da (Daltons).


High Throughput: Accommodates up to 40 multiplexes within a single tube, facilitating efficient processing.

Cost-Effectiveness: Eliminates the need for modifications like fluorescent probes, thus reducing overall expenses.

Short Cycle Time: From DNA conversion to data reporting, the process can be completed within 8-10 hours, ensuring swift results.

High Typing Accuracy and Sensitivity: Provides precise and sensitive SNP typing results.


Special Instrumentation Required: Necessitates specialized instrumentation for implementation.

Limited Detection Scope: Unable to identify unknown mutations, restricting its utility in certain contexts.

Sample and Loci Requirements: Imposes specific criteria for samples and loci per test, which may constrain flexibility and scalability.

  • Multiplex SNaPshot Detection Method

SNaPshot technology, also known as minisequencing, resembles first-generation sequencing. In a reaction system containing DNA polymerase, four fluorescently labeled ddNTPs, and different-length extension primers adjacent to SNP loci, extension terminates after incorporating a single nucleotide.

Advantages: Flexible, allowing for the design of different-length extension primers for multiple SNP genotyping in a single reaction.

Disadvantages: Higher cost.

  • Genotyping by Sequencing

Next-generation sequencing platforms provide comprehensive genomic data, allowing for the identification of SNPs, INDELs, and structural variations.

Many researchers still opt for the direct sequencing method when studying SNP loci. The Sanger sequencing principle, also known as the dideoxy termination method, faithfully extends the nucleotide sequence along the template strand. SNP occurrences manifest as peak patterns in sequencing results.

high-throughput SNP detection methods primarily encompass whole genome resequencing (WGS), SNP microarrays, and simplified genome sequencing.

Whole genome resequencing (WGS) offers comprehensive coverage of mutation sites within the genome but comes with a high sequencing cost. SNP microarrays are constrained by the number of detection markers and can solely identify existing mutations. Conversely, simplified genome sequencing technology boasts a wider array of detection sites and isn't limited by species, yet its genome coverage remains relatively low at around 2%.

Targeted capture sequencing and low-coverage whole-genome resequencing (LcWGS) present a compelling approach to maximizing the typing price ratio while ensuring precise screening. This approach efficiently delves into germplasm resources at both the molecular biology and breeding utilization levels, thereby fostering advancements in molecular breeding practices.

Advantages: Direct sequencing is the most intuitive and accurate SNP genotyping method, suitable for discovering unknown SNP loci and detecting small sample sizes or a limited number of polymorphic sites.

Disadvantages: Limited throughput and relatively high costs. However, with the rapid development of high-throughput sequencing technologies, even high-throughput sequencing of targeted fragments or whole genomes revitalizes the direct sequencing method.


Genotyping revolutionizes our understanding of genetics and its applications across diverse disciplines. From personalized medicine to agricultural advancements, genotyping empowers researchers and practitioners to make informed decisions based on an individual's or population's genetic profile.

Questions & Answers

  • How does genotyping contribute to personalized medicine?

Genotyping enables clinicians to identify genetic variations associated with disease susceptibility and drug response, facilitating personalized treatment strategies tailored to individual patients.

  • What role does genotyping play in crop improvement?

In agriculture, genotyping assists breeders in identifying desirable genetic traits, accelerating the development of crops with improved yield, disease resistance, and nutritional content.

  • What are the limitations of genotyping technologies?

While genotyping technologies offer valuable insights into genetic variations, they may have limitations in detecting rare or complex genetic variants accurately. Additionally, ethical considerations regarding privacy and consent are crucial when utilizing genetic information for research or clinical purposes.

For Research Use Only. Not for use in diagnostic procedures.
Related Services
Quote Request
! For research purposes only, not intended for personal diagnosis, clinical testing, or health assessment.
Contact CD Genomics
Terms & Conditions | Privacy Policy | Feedback   Copyright © CD Genomics. All rights reserved.