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 TaqmanAllelic Discrimination Assay

Feature:
Applied Biosystems’s (ABI) Taqman Assay is performed using ABI Prism 7900 HTSequence Detection System, which allows single-plex SNP interrogation throughfluorescence detection in real-time PCR.

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Pricing
  • Set-upFee: 
  • $250 perSNP (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 GenotypingPlatform

 

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

Pricing

 

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

 

Contact:
Hardeep K. Ranu, PhD
Genotyping Manager
Program in Genetic Epidemiology and Statistical Genetics
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, trialprimer and assay design will be carried out and a trial genotyping runperformed. Depending on those results, we will either proceed with full-scalegenotyping or consider alternative genotyping methods as necessary. Qualitycontrol 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, SampleHandling, and Whole Genome Amplification Service

 

II.1. DNA Extraction andSample Handling

 

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

 

Pricing

  • Extraction Cost:
  • $13per 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 GenomeAmplification

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Feature:
Whole genome amplification using the GenomiPhi DNA Amplification Kit fromAmersham Biosciences is used to amplify linear genomic DNA by MultipleDisplacement Amplification (MDA). This Kit is based on the high processivity,high fidelity, and strand displacement ability of bacteriophage Phi29 DNApolymerase. The typical yield is 3-7 micrograms of amplified DNA from as littleas 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 Genetic Epidemiology and Statistical Genetics
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