Viral / Molecular Core High Density Sequencing Support
Core Services Main Page | Virology | Molecular | Sequencing | SGA Services | BSL-3 Facility | Other
High density sequencing is an emerging technology with the capacity to generate millions of sequences, with up to a billion bases of sequence in a single run. This approach is ideal for application to complex genetic populations such as HIV and SIV, HBV/HCV, complex bacterial populations and other applications.
The Viral/Molecular Core is now offering 454/Roche pyrosequencing as a service. In each case, amplicons will be generated from samples of interest, then sample sequences determined. Runs typically yield ~100,000 sequence reads of >250 bp with good quality scores. Runs are typically divided up among 46 bar-coded individual samples, but can be utilized for fewer samples if greater depth is needed. Sequences are subject to stringent quality control algorithim and provided to users in fasta format. The core also provides advice on experimental design, sequence work up, statistical analysis, and long term data storage.
Several services are offered.
- Initial consultation on experimental design (free of charge)
- Deep sequencing of HIV-1 viral genomes
- Deep sequencing of bacterial 16S rRNA gene sequence tags
- Programmer time for data analysis
- Optimized bar-coded primers for amplification
Pricing
The Core provides support for each of these areas thought the expertise of Dr. Rick Bushman (Core Co-Director). Advanced bioanalytic support and analysis is offered collaboratively through the Biostatistics and Data Management Core (Core G) by Dr. Hongzhe Li (Core G Co-Investigator).
For further information on utilizing V/M Core support for high density sequencing, contact Dr. Rick Bushman.
Core Service Contact:
Frederic Bushman, Ph.D.
Core Co-Director, Viral and Molecular
Core
Phone: 215-573-8732
Email: bushman@mail.med.upenn.edu
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Pricing
Prices below are for CFAR members. Prices are also available for outside users--please contact core staff for details.
| Junior Run from bar-coded Amplicon (average ~100,000 sequence reads; up to 46 samples) |
$2220 |
| Bar coded amplicon prep from DNA (46 samples) | $722 |
| HIV-1 cDNA from plasma or tissue culture virus | $20/sample |
| 16S or HIV bar-coded primers (per set of 50) | $300 |
| Programmer Time (per hour) | $90/hr |
Price comparison
Our cost per sample starting with DNA, is about $64 per sample with average of 2000 sequences per sample (based on average Junior run with recommended 46 samples).
For comparison, analysis of bacterial populations is also available commercially from Second Genome, Inc. Costs per sample vary from $574 to $206 per sample depending on volume.