For customers interested in individual variants, the GRCF offers custom genotyping to analyze short tandem repeats (STR), variable number tandem repeats (VNTR) and single nucleotide polymorphisms (SNP). SNP detection can be done using various methods:
- TaqMan analysis with custom or predesigned kits on an Applied Biosystems 7900HT Real Time PCR System
- Sanger sequencing of PCR products on an Applied Biosystems 3730XL DNA Analyzer
- Pyrosequencing of PCR products on the Qiagen Pyromark Q24 using custom or predesigned kits
Below is a partial list of polymorphisms that have been developed.
|Alpha2C adrenergic receptor||ADRA2C||12bp in frame deletion Del322-325|
|Angiotensin I-converting enzyme||ACE||insertion/deletion polymorphism|
|Apolipoprotein E||APOE||112T>C and 158C>T (E2, E3, E4 alleles)|
|Asporin||ASPN||aspartic acid (D) repeat GAT|
|Dopamine Receptor D4||DRD4||48bp VNTR|
|Dopamine Transporter||DAT/SLC6A3||40bp VNTR in 3'-untranslated region|
|Monoamine oxidase A gene||MAOA||30bp VNTR in promoter|
|Serotonin transporter||5'-HTTLPR||insertion/deletion (Long/Short allele)|
Pricing is sample number and project dependent for individual variant projects. Please contact Laura Kasch for consultation and a quote.
If you wish to do your own Taqman genotyping, but don’t have the equipment to read the results, you may rent time on our self-service equipment.
$20/hour to thermocycle on the machine, $10 for an endpoint read (half hour time block).
Taqman OpenArray Chemistry from Life Technologies. The OpenArray technology spots off-the-shelf or custom Taqman assays into 33 nl throughholes on arrays, allowing many SNPs to be tested on the same sample at once. Each chip assays 12-144 samples, depending on format. Chips may be formatted for 12, 28, 60, 120, 180 or 240 SNPs. Please contact Roxann Ashworth [410-614-0702] for SNP selection.
The minimum of chips that must be ordered varies by SNP number, but for smaller numbers of SNPs, these arrays are often very cost effective, even if all of the chips won’t all be used. Pricing in table is for the minimum number of chips, assumes that some SNPs will be custom designs and that all chips will be used. Chip designs using only inventoried assays are slightly cheaper. The price shown includes data cleaning to ensure the accuracy of returned genotypes. Actual prices will be adjusted based on the number of chips used.
PLINK output and detailed metrics (error rates, unexpected duplicate analysis, etc) are available for this service for an additional $600.
|Chip Format||# Samples/Chip||Minimum # of Chips|
|12 SNPs||144||10 (1440)||Chips: $7,100|
Other costs: $2,975
|26 SNPs||96||10 (960)||Chips: $7,000|
Other Costs: $2,860
|60 SNPs||48||20 (960)||Chips: $13,480|
Other costs: $3,650
|120 SNPs||24||40 (960)||Chips: $27,000|
Other costs $7,300
|180 SNPs||16||60 (960)||Chips: $40,440|
Other costs: $10,950
|240 SNPs||12||80 (960)||Chips: $54,160|
Other costs: $14,600
iSelect Infinium BeadChips: The Infinium technology is the same technology as used for the Genome Wide Association Chips. These custom panels can be created using between 3,000 and 1,000,000 SNPs, for any species with sequence information. The minimum number of samples for this to be cost-effective is 1,100. Custom content can also be added to any of Illumina’s GWAS chips, often at a lower cost than a completely custom chip.
Pricing on this product is based on increments of both SNP numbers and sample numbers. Please contact Roxann Ashworth [410-614-0702] for detailed information on pricing and SNP selection.
Note: When selecting SNPs for this platform, one should select as many SNPs as possible within the appropriate increment, as Illumina estimates up to 20% of the selected SNPs will fail the manufacturing process and will not be placed on the custom chip. The SNP number calculations are further complicated by the fact that there are two different forms of the Infinium chemistry, one of which requires two bead types, the other of which requires only one. Bead types need to be counted when the final number of SNPs in selected. This information is provided by Illumina when the SNP selection files are returned.