Individual Variants                                      Self-Service Genotyping
Medium Throughput Options                 High Throughput Options

Individual Variants

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 biotinlyated PCR products on the Qiagen Pyromark Q24, using custom or predesigned kits

In addition to the kits offered by Life Technologies and Qiagen, we have developed assays for some common polymorphisms.

GeneGene SymbolDescription
Alpha2C adrenergic receptorADRA2C12bp in frame deletion Del322-325
Angiotensin I-converting enzymeACEinsertion/deletion polymorphism
Apolipoprotein E APOE112T>C and 158C>T (E2, E3, E4 alleles)
Asporin ASPNaspartic acid (D) repeat GAT
Dopamine Receptor D4DRD448bp VNTR
Dopamine TransporterDAT/SLC6A340bp VNTR in 3'-untranslated region
Monoamine oxidase A geneMAOA30bp VNTR in promoter
Serotonin transporter 5'-HTTLPRinsertion/deletion (Long/Short allele)
Serotonin transporter 5'-HTTLPRrs#25531, A>G SNP

Pricing:

Pricing is sample number and project dependent for individual variant projects. Please contact Laura Kasch [410-614-3830] for consultation and a quote.

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Self-Service Genotyping

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.

Pricing:

$15/hour to thermocycle on the machine, $10 for an endpoint read.

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Medium Throughput

We offer both Taqman OpenArray chemistry for assessing multiple SNPs on a minimum of 90 samples.

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.

Pricing:

A 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 they won’t all be used.  Pricing in table is for the minimum number of chips and assumes that all chips will be used.  Pricing includes data cleaning to ensure the accuracy of returned genotypes.  Actual prices will be adjusted based on the number of chips used.

Chip Format# Samples/ChipMinimum # of Chips
(Samples)
PriceTotal cost
12 SNPs14410 (1440)Chips: $5,728
Other costs: $2,100
$7,828
26 SNPs9610 (960)Chips: $5,728
Other Costs: $2000
$7,728
60 SNPs4820 (960)Chips: $11,456
Other costs: $2,700
$14,156
120 SNPs2440 (960)Chips: $22,912
Other costs $5,400
$28,312
180 SNPs1660 (960)Chips: $34,368
Other costs: $8,100
$42,468
240 SNPs1280 (960)Chips: $45,824
Other costs: $10,800
$56,624

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High Throughput Options

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.  For more information on the chemistry, see Illumina’s website.

Pricing:

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.

Affymetrix custom arrays:  These arrays can be ordered in two sizes: less than 50K SNPs and less than 750K.  There is a minimum order of 570 samples.

Pricing:
Number of SNPs
(570 sample minimum)
Price range
(per sample)
>50K SNPs$145-$200
>750 SNPs$210-$280