Genotyping
TaqMan OpenArray Genotyping System
The TaqMan OpenArray Genotyping System from Applied Biosystems uses fluorescence-based polymerase chain reaction (PCR) reagents to provide qualitative detection of targets using post-PCR analysis. Three types of TaqMan assays can be ordered from Applied Biosystems:
- TaqMan SNP genotyping assays
- Custom TaqMan SNP genotyping assays
- TaqMan drug metabolism genotyping assays
- The TaqMan SNP genotyping assays library consist of two human and one mouse assay collections, and can be supplemented with assays design with the Custom TaqMan SNP genotyping assays. To submit the custom target sequences, please log on to http://www.appliedbiosystems.com/filebuilder.
- TaqMan drug metabolism genotyping assays: Polymorphisms in drug metabolizing enzymes may influence the rate of foreign compound metabolism and/or excretion among individuals, thereby potentially affecting foreign compound efficacy and/or toxicity. The TaqMan drug metabolism genotyping assays detect polymorphisms such as SNPs, insertions and deletions, and multiple-nucleotide polymorphisms in the genes that code for the drug metabolism enzymes and drug transporters. About 220 genes are included in this assay set. If your SNP of interest is not available in that assay, it may be available in the “TaqMan SNP genotyping assay”. Please look at the following website to search for your gene of interest: https://www5.appliedbiosystems.com/tools/cadt/.
Overview
- Perform genotyping experiments to identify slight variation in genes within a population
- Provide PCR-based end point analysis of tens to hundreds of single nucleotide polymorphism (SNP) across thousands to tens of thousands of samples.
- Each TaqMan OpenArray genotyping plate is preloaded with 16 to 256 TaqMan assays.
- There are 3072 reaction through-holes in the plate. Individual through-holes are preloaded with a TaqMan assay and can accommodate a 33 nl reaction volume.
- Each TaqMan plate is divided into 48 subarrays. Each subarray consists of 64 through-holes. Each through-hole may contain a single assay.
- The number of assays in the TaqMan OpenArray plate and the number of samples that can be loaded in the plate vary depending on the format selected.
TaqMan OpenArray Genotyping Plates Format available from Applied Biosystems
| Format | # of assays preloaded per TaqMan OpenArray plate | Max # of samples per plate | Volume of DNA needed per well when transferring to different format plates | # of sample plate needed to fill the OpenArray plate | Samples in sample plate |
|---|---|---|---|---|---|
| 16 | 16 | 144 | 1.5 ul | 3 | Sample plate 1: 1-48 Sample plate 2: 49-96 Sample plate 3: 97-144 |
| 32 | 32 | 96 | 2 ul | 2 | Sample plate 1: 1-48 Sample plate 2: 49-96 |
| 64 | 64 | 48 | 2.5 ul | 1 | Sample plate 1: 1-48 |
| 128 | 128 | 24 | 2.5 ul | 1 | Sample plate 1: 1-48 |
| 192 | 192 | 16 | 2.5 ul | 1 | Sample plate 1: 1-48 |
| 256 | 256 | 12 | 2.5 ul | 1 | Sample plate 1: 1-48 |
*Plates can only be ordered in packs of 10.
Requirements
- The TaqMan OpenArray plate requires 250 copies of haploid genome for each individual through-hole reaction.
- A concentration of 50 ng/ul is required for human DNA.
- A 3-20 ng of purified genomic DNA is recommended for the TaqMAn Drug metabolism genotyping assay.
- The same amount of DNA should be use for all the samples run with one assay.
- The DNA should be purified with an optimized protocol, should not contain PCR inhibitors, and should appear intact when visualized by gel electrophoresis.
- The DNA should have a A260/280 ratio between 1.7 and 1.9.
- The DNA will also be quantified using the TaqMan RNAse P detection method.
- All reported dye information is as follow: “A” allele always represents the VIC dye and the “B” allele always represent the FAM dye.
- A *.csv file will need to be provided to GGF to keep track of the samples in each plate. The *.csv template file to be completed by the user can be downloaded here.
How to start an OpenArray with GGF
- Contact GGF to discuss your project
- Order the TaqMan genotyping assay of choice from Applied Biosystems.
- To order TaqMan SNP genotyping assays, please download the following instructions from Applied Biosystems: http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_042456.pdf
- Payment for ordering the TaqMan assay will be between the customer and Applied Biosystems. Note that it can take 3 to 6 weeks before your order is ready and shipped from Applied Biosystems.
- Once you receive your TaqMan assay, please bring it to us with your DNA samples to be tested.
- Set up an account with GGF for future payment of services rendered by GGF.
- The TaqMan genotyping assay will be run by GGF.
- Data will be sent to the customer in *.csv format via e-mail.
- Customers will be charged by GGF to run OpenArray plates according to the Table found below.
Cost
Prices charged to run OpenArrays at GGF
| Assays/ sample | Total #samples | Min number of plates ordered | UGA users | Non-UGA users | Profit users | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total project | First plate* | Subsequent plate | Total project | First plate** | Subsequent plate | Total project | First plate*** | Subsequent plate | ||||||||||||
| 16 | 1440 | 10 | $1,050 | $420 | $70 | $1,208 | $484 | $81 | $1,260 | $484 | $81 | |||||||||
| 32 | 960 | 10 | $1,050 | $420 | $70 | $1,208 | $484 | $81 | $1,260 | $484 | $81 | |||||||||
| 64 | 960 | 20 | $1,750 | $420 | $70 | $2,013 | $484 | $81 | $2,100 | $484 | $81 | |||||||||
| 128 | 960 | 40 | $3,150 | $420 | $70 | $3,623 | $484 | $81 | $3,780 | $484 | $81 | |||||||||
| 192 | 960 | 60 | $4,550 | $420 | $70 | $5,233 | $484 | $81 | $5,460 | $484 | $81 | |||||||||
| 256 | 960 | 80 | $5,950 | $420 | $70 | $6,843 | $484 | $81 | $7,140 | $484 | $81 | |||||||||
