Genomics DNA Genotyping Services
DNA Fingerprinting and Genotyping
Analyses available via the ABI PRISM® 3130 Genetic Analyzer include AFLP (amplified fragment length polymorphism analysis), SSR (simple sequence repeats), and 16S microbial identification scans. With the use of Perkin Elmer’s ABI GeneScan Analysis System, we are able to take advantage of proven multicolor fluorescence technology for sizing and quantitating PCR and other DNA fragments. As in DNA sequencing, GeneScan analyzes four different fluorescent labels visualized as blue, green, yellow, and red. GeneScan Analysis Software automatically identifies all DNA bands, compares the mobility of each band to that of the internal lane standards and then sizes the bands based on the sizing curve of the internal lane standards.
Applications
Amplified Fragment Length Polymorphism (AFLP)
Amplified Fragment Length Polymorphism is a powerful DNA fingerprinting technique that can be used for plants and bacteria based on the selective amplification of restriction fragments from a total digest of genomic DNA.
The technique involves three steps:
- Restriction of genomic DNA and ligation of oligonucleotide adaptors
- Selective amplification of a subset of all fragments in the total digest
- Gel based analysis of the fluorescent amplified fragments
The AFLP is particularly powerful because it requires no prior sequence characterization of the target genome, and is readily applicable to a wide variety of crops with different genome sizes.
The new AFLP Plant Mapping Kit from Perkin-Elmer enables plant researchers to genotype crops for: mapping,marker-assisted selection, trueness to type, varietal identification and backcrossing.
The bacterial kit for microbial fingerprinting allows for:
- Differentiation and tracking of highly related microbes at the species, or strain level
- High-resolution genotyping for taxonomic applications
- Detection of DNA polymorphisms in genome evolution studies
- Determining the relatedness of pathogenic organisms inepidemiological studies
- mapping of cloned fragments in bacterial and yeast artificial chromosomes (BACs and YACs)
Short Tandem Repeats (STR)
This primer set is a panel of fluorescently labeled primer pairs that amplify tetranucleotide short tandem repeats (STR) loci. STR analysis is an important complement to both the length and sequence-based DNA typing systems used for human identification. Because of the small size of STR markers, STR systems can be used successfully to analyze samples containing minute amounts of DNA and degraded DNA that cannot be typed using conventional methods. STR’s can be used for forensic applications, determining population genotype frequencies and constructing DNA databases.
16S microbial identification scans
A powerful method of identifying microbes in mixed populations such as soil and rhizosphere samples.
Fingerprinting Methods
6-FAM, HEX and TET Phosphoamidites for Fluorescently Labeled Oligonucleotides
These enable direct 5’end labeling of primers and probes at coupling efficiencies greater than 90%. These dyes are designed to facilitate genetic analysis and are equally useful in many applications historically employing radioactivity such as in situ hybridization, cell uptake studies and target sequence identification, linkage mapping and gene-expression applications.
(F) dNTP’S
Dye-labeled deoxyribonucleotide triphosphates (f) dNTP’s can be incorporated into both strands of a PCR amplicon at random dC and dT sites and extended by enzymes such as Amplitaq™ DNA polymerase and GeneAmp® thermostable rTth Reverse Transcriptase. (f)dNTP’s consist of either a 2’-deoxyuridine 5’-triphosphate d(UTP) or a 2’-deoxycytidine-5’-triphosphate d(CTP) coupled to one of the following rhodamine dyes:
- r110-blue
- RG6-green
- Tamra-yellow
(F) dUTP’s are an attractive alternative labeling method because you can use your existing PCR primers. There is no need to prepare a fluorescent labeled primer. Also, each labeled PCR product can contain multiple fluorescent labels thereby producing more fluorescent signal per molecule.
Data Retreival
We can transfer your data to a USB, CD or upload to our Finch Server. Data is usually available within 48 hours after submission. Electropherograms can be printed in color, at cost, if requested.
Viewing Data
You can view your electropherograms located under the FSA tab using our Finch Server. There are other freeware programs available. ABI offers Peak Scanner. You can download this free of charge from the ABI website. Genographer and Genescanview are also freeware programs.
DNA Quantity Required
A good range of DNA to aim for is 200-300ng of DNA in a 20uL volume.
Pricing
| Service | Price/ Run of 16 |
|---|---|
| Basic | $73.60 |
| For > 96 samples | call |
Mouse “Tail-Snip” Genotyping
In order to set up your assay, you should first schedule an appointment with the Genomics Core by contacting us.
Please bring along any relevant references or materials in order for us to work out the protocols and prospective pricing. In general, processing time is ~3 days after receipt of tissue and costs $30.00 per set of 12 samples (average).
Submission Guidelines
Tail snips (2-5mm) should be submitted in individual 1.5ml tubes. (Ideally we would like samples submitted in multiples of 12 but this is not absolutely required)
Workflow
The samples are digested overnight in proteinase K and prepped on our Autogen 850α DNA isolation system.
The purified DNA is then subjected to the appropriate PCR based genotyping assay.
