SNP Genotyping
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 on understanding and treating disease.
SNaPshot data
Experimental Workflow: Find the Products You Need for Every Step
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Step 1:
Amplify DNA / Purify Template -
Step 2:
Primer Design / Amplification -
Step 3:
Sample Cleanup -
Step 4:
Sequencing Reaction -
Step 5:
Reaction Cleanup -
Step 6:
Electrophoresis -
Step 7:
Analyze Data
Click the arrows above to view products
Step 1: Amplify DNA / Purify Template
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.
Products for Step 1: Amplify DNA / Purify Template
- Centri-Sep™ Columns
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Centri-Sep™ spin columns are used for the fast and efficient purification of nucleic acids. The Centri-Sep gel provides excellent recovery of DNA fragments larger than 16 base pairs, while removing greater than 98% of salts, NTP's and other unwanted low-molecular-weight impurities.
Step 2: Primer Design / Amplification
Many common DNA sequencing workflows require you to amplify your extracted DNA sample before sequencing. To amplify your DNA sample, you need DNA polymerase (such as AmpliTaq® Gold DNA Polymerase), nucleotides (dNTPs), reaction buffer, primers, and a thermal cycler.
Products for Step 2: Primer Design / Amplification
Step 3: Sample Cleanup
After PCR amplification, the resulting template is in solution, along with primers, dNTPs, and enzyme and buffer components. To avoid participation in the subsequent primer-extension reaction, primers and unincorporated dNTPs must be removed.
Step 4: Sequencing Reaction
Cycle sequencing is a simple method in which successive rounds of denaturation, annealing, and extension in a thermal cycler result in linear amplification of extension products. The products are then injected into a capillary. All current Applied Biosystems DNA sequencing kits use cycle sequencing protocols. For de novo sequencing we recommend Dye Terminator chemistry.
Products for Step 4: Sequencing Reaction
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BigDye® Terminator v1.1 Cycle Sequencing Kits
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BigDye® Terminator v1.1 Cycle Sequencing Kits are designed for specialty applications that require optimal basecalling adjacent to the primer and for sequencing short PCR product templates with rapid electrophoresis run modules.
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BigDye® Terminator v3.1 Cycle Sequencing Kits
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The BigDye Terminator v3.1 Cycle Sequencing Kit's robust, highly flexible chemistry is ideal for de novo, resequencing, and finishing with PCR product, Plasmid, Fosmid, and BAC templates.
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dRhodamine Terminator Cycle Sequencing Kits
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The dRhodamine Terminator Cycle Sequencing Kit provides optimized dRhodamine dideoxy terminators chemistries for decreased background noise in a wide array sequencing applications.
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dGTP BigDye® Terminator Cycle Sequencing Kits
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The dGTP BigDye® Terminator Cycle Sequencing Kit's fluorescent dideoxy terminator chemistry is optimized for sequencing through GT- and G-rich templates.
Step 5: Reaction Cleanup
After the sequencing reaction, it is important to remove unincorporated dye terminators and salts that may compete for capillary electrophoretic injection. Unincorporated terminators can co-migrate with the sequencing template, resulting in basecalling errors, and excess salt translates to poor signal-to-noise ratios.
Products for Step 5: Reaction Cleanup
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BigDye XTerminator® Purification Kit
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The BigDye XTerminator® Purification Kit is a fast, simple purification method for DNA sequencing reactions that removes unincorporated BigDye® terminators. No more dye blobs! Cleanup is complete in under 40 minutes and requires less than 10 minutes of labor.
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SNaPshot® Multiplex System
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The SNaPshot® Multiplex System is a primer extension-based method that enables multiplexing up to 10 SNPs (single nucleotide polymorphisms). Use this system to screen and confirm SNPs, assess DNA methylation, fingerprint BACs, and screen samples for scrapies susceptibility.
Step 6: Electrophoresis
After performing the post-sequencing reaction purification, samples are ready for analysis on an Applied Biosystems capillary electrophoresis-based genetic analyzer. During capillary electrophoresis, the products of the cycle sequencing reaction migrate through capillaries filled with polymer. The negatively charged DNA fragments are size separated as they move through the polymer in the capillaries toward the positive electrode.
Products for Step 6: Electrophoresis
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3500 Genetic Analyzer
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The 3500 8-capillary platform can run a wide variety of applications—including de novo sequencing and resequencing (mutational profiling)—as well as microsatellite analysis, MLPA™, LOH, MLST, AFLP® and SNP validation or screening. The majority of applications can be run on a single polymer and capillary array.
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3500xL Genetic Analyzer
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The 3500xL 24-capillary platform can run a wide variety of applications, including de novo sequencing and resequencing (mutational profiling), as well as microsatellite analysis, MLPA™, LOH, MLST, AFLP® and SNP validation or screening. The majority of applications can be run on a single polymer and capillary array.
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3730 DNA Analyzer
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The 48-capillary 3730 DNA Analyzer is the Gold Standard in medium-to-high throughput genetic analysis.
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3730xl DNA Analyzer
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The 96-capillary 3730xl DNA Analyzer is the Gold Standard for high throughput genetic analysis. Use this for DNA fragment analysis applications such as microsatellites, AFLP, SNP analysis, mutation detection and traditional DNA sequencing. Get the highest quality data at a low cost per sample.
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3130 Genetic Analyzer
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Applied Biosystems 3130 Genetic Analyzer is the latest generation of 4-capillary electrophoresis instruments for the low to medium throughput laboratories. The system offers industry-leading performance, plus sophisticated automation capabilities allowing you to save time, reduce costs and increase productivity.
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3130xl Genetic Analyzer
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Applied Biosystems 3130xl Genetic Analyzer is the latest generation of 16-capillary electrophoresis instruments for the medium throughput laboratories.
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310 Genetic Analyzer
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The ABI PRISM® 310 Genetic Analyzer is an automated single-capillary genetic analyzer designed for a wide range of sequencing and fragment analysis applications.
Step 7: Analyze Data
After electrophoresis, Data Collection software creates a Sample File of the raw data. Using downstream software applications, further data analysis is required to translate the raw data into the corresponding electropherogram.
Products for Step 7: Analyze Data
- GeneMapper® Software
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GeneMapper is a flexible genotyping software package that provides DNA sizing and quality allele calls for all Applied Biosystems electrophoresis-based genotyping systems.
- Peak Scanner™ Software
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Use this free software to perform DNA fragment analysis; separate a mixture of DNA fragments according to their sizes, provide a profile of the separation, and precisely calculate the sizes of the fragments.
- Sequencing Analysis Software
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This software enables you to basecall, trim, display, edit, and print data from our entire line of capillary DNA sequencing instruments for data analysis and quality control.
- Variant Reporter® Software
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The Variant Reporter™ Software performs comparative sequencing, also known as direct sequencing, medical sequencing, PCR sequencing and resequencing with DNA sequencing files. The software is designed for reference based and non-reference based analysis such as mutation detection and analysis, SNP discovery and validation and sequence confirmation.
- SeqScape® Software
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Applied Biosystems SeqScape® software is designed for reference based analysis such as mutation detection and analysis, SNP discovery and validation, pathogen sub-typing, allele identification, and sequence confirmation. This product is also integrated for use with VariantSEQr™ Resequencing Set.
Poster
Product Bulletin
Publications
- A genome-wide association scan of nonsynymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1 Publication: Nature Genetics 39, 207 - 211 (2006)
- Variant Reporter™ 30-day demo version Download Free
- SNPbrowser™ Software Download Free
Training Courses
North American training: Europen training:
