HTP Core 3

Genotyping Core Facility

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Partners Healthcare | Personalized Medicine

Dana-Farber/Harvard Cancer Center 

Director: Immaculata De Vivo, M.P.H., Ph.D.Associate Professor in Medicine

Location: Harvard School of Public Health, 665 Huntington Ave, Bldg II, Boston MA 02115

I. Genotyping Services

I.1. TaqMan Allelic Discrimination Assay

Applied Biosystems (ABI) TaqMan Assay is performed using the ABI 7900HT instrument which allows for single SNP interrogation through fluorescence detection.  The system is run in high-throughput format using 384-well plates, thus providing fast turnaround times for investigators.

7900HT TaqMan qPCR machines (photo by Channing Johnson)

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384 well plates in the lab (photo by Channing Johnson)

Pricing:
TaqMan Set-up Fees: 

Fewer than 700 samples and assay not in stock (DF/HCC): $258
Fewer than 700 samples and assay not in stock: $295

700-3500 samples and assay is in stock (DF/HCC): $420
700-3500 samples and assay is in stock: $480

3500 samples or more and assay not in stock (DF/HCC): $858
3500 samples or more and assay not in stock: $980

TaqMan Genotyping Cost:  

DF/HCC members: $0.60 per SNP per sample
Non DF/HCC member: $0.68 per SNP per sample

Please contact Hardeep Ranu for more information.

I.2. OpenArray SNP Genotyping Platform
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Inside an OpenArray instrument (photo by Channing Johnson)

The 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

OpenArray 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.

 I.3. Targeted Sequencing
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IonTorrent PGM (photo by Channing Johnson)

HTP Core 23

Heat Map of IonChip loading (photo by Channing Johnson)

Targeted sequencing service using the Ion Torrent PGM.

The capabilities of this service include:

Custom Amplicon Sequencing of DNA and RNA Panels

Ready-to-use Ion AmpliSeq Panels:

Cancer Hotspot Panel – 50 genes, > 2,800 Cosmic Mutations, 207 Amplicons
Comprehensive Cancer Panel – 409 genes, 16,000 Amplicons
Inherited Disease Panel – 700 disease, 328 genes, 10,000 Amplicons

The system requires only 10ng of input DNA and DNA from FFPE samples can also be used. Additionally, only one or two samples can be run at a time.

There are three different Chip formats:

  • Ion 314 Chip: 1 million wells,  400-550 thousand reads for 200bp sequencing
  • Ion 316 Chip: 6 million wells, 2-3 million reads for 200bp sequencing
  • Ion 318 Chip: 11 million wells, 4-5.5 million reads for 200bp sequencing

Please contact Hardeep Ranu for more information

I.4. Quality Assurance

Quality control procedures include repeat genotyping of at least 5% of DNA samples. Genotyping results are provided to the user in electronic format. Extensive bioinformatics support for our Core Facility is in place.

For more information on our TaqMan and OpenArray genotyping and Targeted Sequencing services please contact:

Hardeep K. Ranu PhD, Genotyping Manager
Phone: 617-432-4469
Email: hranu@hsph.harvard.edu

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

II.1. DNA Extraction and Sample Handling

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Sample Handling Robot (photo by Channing Johnson)

Sample preparation (photo by Channing Johnson)

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.

Pricing:

  • $20 per 50-200 ul WBCs, buccal cells, or whole blood (non-DF/HCC)
  • $17.51 per 50-200 ul WBCs, buccal cells, or whole blood (DF/HCC discount)

Please contact Pati Soule for more information on this service

II.2. Whole Genome Amplification

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Sample aliqioting (photo by Channing Johnson)

Whole genome amplification using the GenomiPhi DNA Amplification Kit from GE 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:

  • $18 per sample (2 ul of 5 ng/ul) for a single reaction (non-DF/HCC)
  • $15.76 per sample (2 ul of 5 ng/ul) for a single reaction (DF/HCC discount)

Please contact Pati Soule for more information on this service.

II.3. Telomere Length Analysis

Please contact Pati Soule for more information on this service.

For more information and pricing on DNA Extraction, Whole Genome Amplification and Telomere Length analysis services please contact:
Patrice Soule, Lab Manager
Phone: 617-432-6101
Email: psoule@hsph.harvard.edu

All prices quoted are for internal HSPH or Partners investigators only.  For external customers please contact Hardeep Ranu (genotyping or targeted sequencing services) or Pati Soule (DNA extraction, Whole genome amplification or Telomere length analysis services) for further information regarding pricing.