Program in Molecular and Genetic Epidemiology

Genotyping Core Facility

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Harvard-Partners Center for Genetics and Genomics, Dana-Farber/Harvard Cancer Center 

 

I. Genotyping Service

 

I.1. ABI Prism Taqman Allelic Discrimination Assay

Feature:
Applied Biosystems's (ABI) Taqman Assay is performed using ABI Prism 7900 HT Sequence Detection System, which allows single-plex SNP interrogation through fluorescence detection in real-time PCR.

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Pricing
  • Set-up Fee:         
  • $250 per SNP (for < 700 DNA samples)
  • Taqman Genotyping Cost:  
  • $465 per SNP (for assays currently in stock)
  • $905 per SNP (for assays currently not in stock)
  • $0.60 per SNP per DNA sample (not DF/HCC)
  • $0.50 per SNP per DNA sample (DF/HCC discount)
I.2. Biotrove SNP Genotyping Platform

 

Feature:
We now offer a new genotyping service from Biotrove. The Biotrove OpenArray SNP Genotyping Platform allows researchers to run 16, 32 or 64 Taqman assays on one OpenArray chip. The OpenArray chips require only 33nl of assay allowing for significant cost savings.
 

Pricing

 

Biotrove Genotyping Cost: As pricing varies according to the number of samples and number of SNPs that are run, please contact Hardeep Ranu for pricing information.

 

Contact:
Hardeep K. Ranu, PhD
Genotyping Manager
Program in Molecular and Genetic Epidemiology
Department of Epidemiology
Building II, Room 255
Harvard School of Public Health
655 Huntington Avenue
Boston, MA 02115
Phone: 617-432-4469
Fax: 617-432-1722
Email: hranu@hsph.harvard.edu


I.3. Quality Assurance

 

For SNPs with existing assays, please visit the following website.

 

For new SNP assays, trial primer and assay design will be carried out and a trial genotyping run performed. Depending on those results, we will either proceed with full-scale genotyping or consider alternative genotyping methods as necessary. Quality control procedures include repeat genotyping of at least 5% of DNA samples. Genotype results are provided to the user in electronic format. Extensive bioinformatics support for our Core Facility is in place.

 

II. DNA Extraction, Sample Handling, and Whole Genome Amplification Service

 

II.1. DNA Extraction and Sample Handling

 

Feature:
DNA extraction is performed using QIAmp Blood Kit (Qiagen, Inc.). We have been successful extracting DNA from WBCs, whole blood, blood spots, residual red cell samples and buccal cells. We currently use the Qiagen company protocol which yields high quality DNA in 200ul of buffer ranging from 5-50ng/ul. The concentration and plating or tube storage is included in the cost. We have 3 robots that assist in protocol set up and sample plating.

 

Pricing

  • Extraction Cost: 
  • $13 per 50-200 ul WBCs, buccal cells, or whole blood (non-DF/HCC)
  • $11 per 50-200 ul WBCs, buccal cells, or whole blood (DF/HCC discount)

II.2. Whole Genome Amplification

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Feature:
Whole genome amplification using the GenomiPhi DNA Amplification Kit from Amersham Biosciences is used to amplify linear genomic DNA by Multiple Displacement Amplification (MDA). This Kit is based on the high processivity, high fidelity, and strand displacement ability of bacteriophage Phi29 DNA polymerase. The typical yield is 3-7 micrograms of amplified DNA from as little as 10-20 ng of genomic DNA template.

Pricing

  • WGA Amplification Cost:  
  • $13 per sample (2 ul of 5 ng/ul) for a single reaction (non-DF/HCC)
  • $11 per sample (2 ul of 5 ng/ul) for a single reaction (DF/HCC discount)

Contact:
Patrice Soule
Lab Manager
Program in Molecular and Genetic Epidemiology
Department of Epidemiology
Building II, Room 226
Harvard School of Public Health
655 Huntington Avenue
Boston, MA 02115
Phone: 617-432-6101
Fax: 617-432-1722
Email: psoule@hsph.harvard.edu