Frequently Asked Questions
1. What is genotyping?
Genotyping is characterisation of an organism in terms of its heritable material, DNA.
2. What is Microsatellite Genotyping?
Microsatellites, also called short tandem repeat sequences (STRs) are regions of DNA where the base sequence is repeated. The most common repeats in humans are dinucleotide repeats but tri- and tetranucleotide repeats are common. The repeating pattern can be up to 7 bases in length. We use microsatellite markers to characterise an organism.
3. How is Microsatellite genotyping done?
Genotyping using microsatellite markers involves PCR amplification of the microsatellite region and measurement of the size of the amplified fragment. For a genome-wide scan we use fluorescently labelled primers for the PCR that amplify 400 microsatellites spread across the human genome. These markers are spread at an average genetic distance of 10 cM. We also have a set of primers that amplify markers spread at 5 cM.
4. What is SNP genotyping and would it benefit my research?
SNP typing is a method of identifying and characterising single base changes. SNP applications are broad ranging, playing a significant role in important aspects of human health such as disease predisposition, quantitative trait linkage in field crops and domestic herds, pharmacogenomics / drug metabolism, evolutionary genetics and forensics.
The research currently being done is highly diverse, therefore if you would like to know whether SNP genotyping will benefit your research we recommend that you contact us, to discuss your requirements.
5. What information will SNP genotyping give me?
The AGRF SNP genotyping service enables researchers to detect single base pair mutations in populations. These mutations are often linked to various phenotypes and can also be used as genetic markers. Once the results have been analysed and checked, the client will receive an email detailing all results - please refer to the Result Formats page for further information.
6. Do you do fine mapping?
AGRF can fine map any region of any DNA.
7. Do you only do studies using human DNA?
Genotyping can be performed on any sample of DNA. Studies have been conducted by AGRF using a broad range of DNA samples, including samples from:
- human blood
- other human tissues from histology sections
- bovine blood and hair samples
- ovine blood
- wheat
- barley
AGRF also offer a Nucleic Acid Extraction Service. Please refer to the Nucleic Acid Extraction and Amplification page for further information.
8. What material do I need to send for Microsatellite genotyping?
To genotype one individual, the amount of DNA required is dependat on the number of markers to be screened. Please refer to Sample Submission Requirements for further information including formulas to calculate the DNA concentrations required.
9. What factors reduce my success in SNP genotyping?
The most significant factor in reducing the success of SNP genotyping is the quality of DNA. All platforms, whether it be sequencing or SNP genotyping rely on good quality DNA to produce high quality results. Therefore, good quality DNA is expected to give a higher call rate and a greater accuracy per call than poor quality DNA.
10. What is good quality DNA?
Good quality DNA generally has an OD 260/280 ratio of 1.8. Different platforms vary in the minimum quality of DNA they require. However, high quality DNA will yield better quality results for all platforms.
11. What DNA extraction method should I use?
There are a variety of kit based and in-house methods for DNA extraction that can be used. For small numbers of samples the AGRF SNP service recommend commercially available column-based extraction systems. For further information on the most appropriate eluate material (e.g. Tris, EDTA or water), please refer to the Sample Submission Requirements.
12. Can AGRF extract my DNA?
Yes. The AGRF has a comprehensive nucleic acid extraction service for extraction of DNA and RNA from a broad range of sample types. This service caters specifically to the requirements of any downstream AGRF services as well as other platform specifications if required. Please refer to the Quote Request page to generate a quote for this service.
13. Can you analyse DNA from histology slides or mouthwashes?
AGRF can analyse DNA from histology slides and other samples that contain very small amounts of DNA, including mouthwashes and virtually any biological sample. DNA extracted from these sources is still required to be of a certain quality. Please refer to the Sample Submission Requirements for further information.
14. When will you send my results?
Result turn around time is project and platform dependent (i.e. sample number versus SNPs per sample to be processed). Please contact us to obtain specific information regarding turn around times.
15. Is my data confidential?
Access to data is provided via a client login which is password protected. Please refer to the AGRF Policies page for further information.
