Mammalian Genotyping Core

The UNC Mammalian Genotyping Core (MGC):

• Services Offered
• Project Initiation
• Genotyping Procedure
• Quality Control
• Pricing

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Services Offered:

ABI TaqMan SNP Genotyping

Pre-Designed/Validated TaqMan® SNP Genotyping Assays

Custom TaqMan® SNP Genotyping Assays

Illumina BeadArray

SNP Genotyping Service

Whole Genome Genotyping

Focused Content

Standard SNP Panels

Custom-designed SNP Panels

GoldenGate custom panels

iSelect Infinium custom panels

Linkage

Human

Mouse

Copy Number/LOH
Methylation

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Project Initiation:

Investigators are strongly encouraged to schedule a free consultation with us before initiating a genotyping project, preferably while preparing a grant proposal. All steps must be conducted well in order to achieve the best quality of genotyping data, including but not limited to genotyping strategy and design, sample collection, DNA purification, quantitation and aliquoting, genotyping experiments and genotype calling.

Please submit the completed Genotyping Project Information Form.

Services are offered on first-come-first-serve basis, but a project will be started only after all necessary documents, high quality DNA samples* and all reagents are received. Please download the Genotyping Project Checklist for a step-by-step guideline.

*DNA Preparation Requirements

• DNA Preparation Requirements for TaqMan SNP Genotyping
• DNA Preparation Requirements for GoldenGate SNP Genotyping

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Genotyping Procedure:

1. Check the electronic version sample sheet(s) prepared by investigator.
2. Receive DNA samples, double check DNA concentration with NanoDrop® ND-1000 UV-Vis Spectrophotometer.
3. Receive ABI TaqMan® SNP Genotyping Assays or Illumina reagents and make inventory.
4. Validate the quality of DNA and assay through testing two TaqMan assays or one plate of DNA with one Illumina OPA (The Oligo Pool ).
5. Perform all the genotyping experiments.
6. Check quality of each experiment immediately after it is competed.
7. Call Allele/genotype with ABI SDS software for TaqMan genotyping or with Illumina BeadStudio for BeadArray genotyping. All SNPs will be thoroughly reviewed by an experienced MGC researcher for TaqMan and GoldenGate assays to ensure the highest possible data quality.
8. Open controls will be evaluated during analysis.
9. Submit report(s) and genotyping data with standard format (other format may be available per request).
10. Recheck data if error rate is unacceptable, which is either estimated by investigator through checking blind controls or by MGC through open controls.

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Quality Control:

Besides rigorous quality management, the following quality control is implemented.

TaqMan SNP genotyping: 4 open controls per 96-well-plate will be provided by MGC for internal quality control, including two positive and two blank controls.

GoldenGate SNP genotyping on the 96-sample Sentrix® Universal Array Matrix platform: 4 open controls per 96-well-plate will be provided by MGC for internal quality checking, controls include both replicates and trios.

Investigators are recommended to include blind controls to estimate genotyping error rate and evaluate genotyping data quality.

The GoldenGate assays implement sophisticated internal controls to ensure high data quality, including allele-specific extension, PCR uniformity, extension gap, gender, first hybridization controls, second hybridization controls, and contamination detection controls. In addition, BeadStudio software provides statistical tools to calculate success for assay development and genotyping confidence levels.

 

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Pricing:

MGC offers very competitive pricing for all UNC Chapel Hill researchers. Please contact us to discuss your project. More accurate cost can be estimated after learning more about your project.