SNP genotyping identifies single nucleotide polymorphisms (SNPs) that are common DNA variants present across the human genome. SNPs have been shown to be responsible for differences in genetic traits, susceptibility to disease, and response to drug therapies.

Genotyping of SNPs has become extremely important to researchers working to understand and treat disease. SNPs occur approximately once every 100 to 300 bases and can be detected by various different techniques such as RFLP, SSCP, sequencing, and more.

Figure 1. SNaPshot® labeling chemistry relies on single-base extension and termination. The SNaPshot® Multiplex Kit uses a single-tube reaction to interrogate SNPs at known locations. The chemistry is based on the dideoxy single-base extension of an unlabeled oligonucleotide primer (or primers). Each primer binds to a complementary template in the presence of fluorescently labeled ddNTPs and DNA polymerase. The polymerase extends the primer by one nucleotide, adding a single ddNTP to its 3´ end. The fluorescence color readout reports which base was added.

The SNaPshot® Multiplex System is a primer extension-based method developed for the analysis of SNPs. Through its multiplexing capability, up to 10 SNPs can be analyzed in a single reaction, regardless of their positions on the chromosome or the amount of separation from neighboring SNP loci. The ability to use unlabeled user-defined primers allows researchers to incorporate SNPs of interest cost-effectively. The Multiplex Ready Reaction Mix (included in the system) helps ensure robust, reproducible analyses of multiplexed samples. Researchers can analyze more than 23,000 SNP genotypes per day on just one 3730xl Genetic Analyzer.

BAC fingerprinting and methylation analysis could also be performed using SNaPshot ® Mulitplex System.

Go to the Publications & Literature tab below to learn some of the many ways our customers use the SNaPshot®  Multiplex System for their research.

Step-by-Step Guide to SNP Genotyping

DNA Purification kit

DNA extraction is a critical first step in the experimental workflow of DNA Sequencing and Fragment analysis. The overall quality, accuracy and length of the DNA sequence read can be significantly affected by characteristics of the sample itself, and the method chosen for nucleic acid extraction. Ideal methods will vary depending on the source or tissue type, how it was obtained from its source, and how the sample was handled or stored prior to extraction.

Recommended Products: DNA Isolation


Amplify the DNA region containing the SNP of interest.

Recommended Products: Perform PCR


Before SNaPshot reaction, primers and unincorporated dNTPs must be removed.


After SNaPshot reaction, it is important to briefly treat the product with Calf Intestine Alkaline Phosphatase.

Recommended Products: Perform and purify the SNaPshot® reaction

For the SNaPshot® Purification
Calf Intestine Alkaline Phosphatase

An aliquot of the SNaPshot reaction is added to an electrophoresis solution consisting of Hi-Di Formamide and GeneScan LIZ-120 size standard.

Recommended Products: Prepare Sample for Analysis

Capillary Electrophoresis

During capillary electrophoresis, the products of the PCR are injected electrokinetically into capillaries filled with polymer. High voltage is applied so that the fluorescent DNA fragments are separated by size and are detected by a laser/camera system.

Which Electrophoresis Instrument (Genetic Analyzer) Is Right for You?

Number of Capillaries 96 48 24 8 16 4 1
Compatible Applications:
(S) Supported; (A) AB Demonstrated; (C) Customer Demonstrated; (N) Not Supported
SNP Genotyping
- SNaPshot® System A A S S S S S

Determine the SNP genotype

Recommended Products: Data Analysis

GeneMapper® Software

Product Literature


SNP Analysis

SNP Quantification

BAC Fingerprinting


Software Downloads

Highlighted Products for SNP Genotyping:

SNaPshot® Multiplex System

GeneMapper® Software

Visistat reference component