TaqMan SNP Genotyping service
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Illumina SNP Genotyping service
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SNaPshot assays
Sequence based genotyping
Introduction
The facility offers multiple genotyping options for the determination of genotypes at specific positions in the genome (SNPs). We can help you determine which of the technologies we support is most appropriate for your SNP genotyping project. Number of samples to process, number of SNPs to interrogate, and the complexity of the chromosomal segment (GC content, repeats) around the SNPs of interest are all factors to consider before choosing a genotyping platform.
TaqMan SNP Genotyping service
This technology is most appropriate for projects of medium size (24 to 768 samples) requiring the genotyping of up to 100 SNPs.
It is possible to use it with smaller size projects although other technologies might be more economical in this case.
This service begins with the review of the list of SNPs to be genotyped as not all SNPs can be typed using the TaqMan technology.
Once your list of SNPs is finalized we will order SNP assays from Applied Biosystems and begin the genotyping process upon receipt of the assays and your DNA.
We require 30ng of genomic DNA per SNP assay and it must be supplied at 30ng/ul in 96 well plates. A minimum of 10ul is required (300ng) regardless of the number of assays to be performed.
All samples must be at the same concentration and purity for the procedure to give best results. Purity should be assessed spectrometrically and a ratio of OD260/OD280 as close to 1.8 as possible at pH=8.5 should be obtained before submitting samples.
The facility runs the standard TaqMan protocol as recommended by the manufacturer, which is successful for the majority of the SNP assays.
However, you may see a decrease in the call rate for a small number of "difficult" assays. The turnaround time for TaqMan projects is usually three days for up to 1,000 genotypes once all the materials have been received.
SNP assays costs from $200 to $375 apiece and are sufficient for processing up to 1500 samples. In addition, there is a charge of $0.65 for each requested genotype.
Illumina SNP Genotyping service
The Illumina Beadstation platform offers great flexibility for high throughput SNP genotyping. Two types of highly multiplexed, microarray-based assays are available:
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The GoldenGate assay allows the multiplexed genotyping of 96, 384, 768 or 1536 SNPs of your choice from a library of over one million SNPs into a custom genotyping set. Optimal project sizes are in multiples of 96 samples.
The facility has developed software to select SNPs from the Illumina library for a variety of applications:- Refinement of linkage in specific chromosomal areas
- Association studies after linkage analysis
- Candidate gene interrogation
- Linkage disequilibrium mapping
Pricing for the Illumina GoldenGate genotyping:
The pricing for projects depends on the number of samples and the number of SNPs to interrogate, starting at $0.06/genotype for custom GoldenGate assays.
Total project cost by sample size and number of SNPs number of samples 96 192 288 384 480 576 number of SNPs 96 $6,564 $10,794 $15,024 $19,004 $22,984 $26,714 384 $12,516 $17,446 $22,376 $27,056 $31,736 $36,166 768 $20,752 $26,582 $32,412 $37,992 $43,572 $48,902 1536 $36,624 $43,654 $50,684 $57,464 $64,244 $70,774 number of samples 672 768 864 960 1056 1152 number of SNPs 96 $30,684 $34,164 $37,644 $40,874 $44,104 $47,084 384 $41,556 $45,736 $49,916 $53,846 $57,776 $61,456 768 $56,152 $61,232 $66,312 $71,142 $75,972 $80,552 1536 $81,144 $87,424 $93,704 $99,734 $105,764 $111,544
Cost per genotype (in cents) by sample size and number of SNPs number of samples 96 192 288 384 480 576 672 768 864 960 1056 1152 number of SNPs 96 71.2 58.6 54.3 51.6 49.9 48.3 47.6 46.3 45.4 44.4 43.5 42.6 384 34.0 23.7 20.2 18.3 17.2 16.4 16.1 15.5 15.0 14.6 14.2 13.9 768 28.1 18.0 14.7 12.9 11.8 11.1 10.9 10.4 10.0 9.6 9.4 9.1 1536 24.8 14.8 11.5 9.7 8.7 8.0 7.9 7.4 7.1 6.8 6.5 6.3
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The Infinium assay allows the multiplexed genotyping of thousands of SNPs pre-selected across the genome for any number of samples. The different array sizes have specific applications like linkage analysis, LOH mapping, molecular karyotyping and whole genome associations. Currently offered Infinium arrays are:
- Human-1 Genotyping BeadChip with over 109,000 SNPs featuring exon-centric content (2/3 of the SNPs are within 10kb of coding sequences)
- HumanCNV370 Genotyping BeadChip containing over 317,000 tag SNPs derived from the Phase I HapMap data (including 8,000 nsSNPs (amino-acid changing SNPs) and a high density of SNPs across the Major Histocompatibility Complex (MHC)) as well as 50,000 Copy Number Variant loci
- HumanHap610 Genotyping BeadChip containing over 610,000 SNP markers provides comprehensive genomic coverage of SNPs and unrivaled access to both known and novel CNV regions.
- Human1M Genotyping BeadChip, provides over 1 million features on a single microarray giving the most comprehensive genomic coverage of any product currently available.
The Infinium assay requires 250ng to 1ug of DNA per sample and most projects of up to 96 samples can be completed within 3 weeks.
Pricing for the Illumina Infinium genotyping service:- The Human-1 BeadChip service is discontinued
- from $365 per sample for the HumanCNV370 array
- from $460 per sample for the HumanHap610 array
- from $775 per sample for the Human1M array
Pricing for Human Linkage Mapping set (6000+ SNP markers - Infinium assay) is $145 per sample.
Contact us at (513) 636-0122 for volume discounts.
SNaPshot assays
The ABI SNaPshot SNP genotyping method is a single nucleotide extension assay at the position of the polymorphic base. Up to 10 SNPs can be detected simultaneously from one or more PCR products. It is a lower cost alternative to sequence based genotyping for the interrogation of multiple known SNPs in a small number of samples. The service includes primers and probes design, PCR optimization and mutation scoring.
Contact us for more information and pricing regarding the SNaPshot genotyping service.Sequence based genotyping
Almost any variation in the genome can be determined by DNA sequencing.
For small projects or in circumstances when other methods have failed to generate data, sequencing may be used for SNP or other variation genotyping.
The service includes design of PCR and sequencing primers, optimizations and mutation scoring.
Contact us for more details and pricing regarding the sequence based genotyping service.