Scientists employing genotyping analysis are looking to untangle the complex relationships between genotype and phenotype in studies focusing on single nucleotide polymorphisms (SNPs), insertion or deletion polymorphisms (indels), and copy number variants (CNVs).

SNPs are heritable single base pair variations that occur throughout an organism’s genome and are the most common form of genetic variation in humans. SNPs underlie traits such as height, response to drugs, and risk of developing diseases. SNP genotyping can help us understand the mechanisms of disease, predict an individual's risk of developing certain diseases, and even help in the design of personalized therapies.

Indels are defined as the insertion or deletion of a small number of bases in a genome and are the second most common class of mutation in the human genome. Indels can have significant effects on gene expression, causing a frameshift mutation (unless the indel length is a multiple of three), and have been implicated in genetic diseases.  

CNVs are variations in the number of copies of a specific gene between individuals and are found in all humans as well as other animals and plants. CNVs affect a significant portion of the genome (approximately 12% of the human genome) and include deletions, duplications, and other complex genotyping patterns. These CNVs can influence gene expression and be associated with specific phenotypes and diseases, as observed in microdeletion and microduplication syndromes.

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Learn how to differentiate between homozygous and heterozygous samples using TaqMan Genotyping Assays.

Get answers to the most frequently asked qPCR questions with our library of quick and easy educational videos covering a variety of topics including experiment setup, best practices, and guidance on products and technologies.

What is genotyping?

What is genotyping?

This article explains what SNPs are and how to detect them, such as with real time PCR. In addition, applications for SNP genotyping are discussed.

Duplexing TaqMan SNP Genotyping Assays

Duplexing TaqMan SNP Genotyping Assays

This article is about the dyes, reagents, and software needed for duplexing a TaqMan SNP Genotyping reaction. It also includes an example with data sets.


Positive Controls for TaqMan SNP Genotyping Experiments

Controls are an important part of TaqMan SNP genotyping experiments. This article goes into detail regarding positive controls, including why you should use them and where to find them.

Quality Value in TaqMan Genotyper Software

The Quality value is an estimate of how closely a given data point belongs to the underlying model of angle and amplitude distribution for each genotype cluster. This technical note explains how the Quality value in TaqMan Genotyper Software is calculated.


Learn how genetic analysis techniques, including sequencing, NGS, and quantitative and digital PCR, are being used by researchers to advance knowledge and innovations in challenging disease and research questions. 


A brief explanation and illustration of how the TaqMan chemistry works in the various applications of gene expression, genotyping, copy number variation, microRNA, mutation detection, and protein quantification.

Additional resources

For Research Use Only. Not for use in diagnostic procedures.