Penn Center for AIDS Research

Viral / Molecular Core High Density Sequencing Support

Core Services Main Page | Virology | Molecular | Sequencing | SGA Services | Intergrated vDNA | 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.

  1. Initial consultation on experimental design (free of charge)
  2. Deep sequencing of HIV-1 viral genomes
  3. Deep sequencing of bacterial 16S rRNA gene sequence tags
  4. Programmer time for data analysis
  5. Optimized bar-coded primers for amplification


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

Ordering Information:
Order High Density Sequencing services through the Path BioResource at Penn. Instructions for the Path BioResource can be found here on the CFAR website or on the Path BioResource site itself.

Core Service Contact:
Frederic Bushman, Ph.D.
Core Co-Director, Viral and Molecular Core
Phone: 215-573-8732


Optimized bar-coded primers for amplification

Tested bar-coded primers are made available to core users as they become available. At present, bar coded 16S V1V2 primers are available as indicated below:

Primer Target
16S V1V2 bacterial rRNA gene
HIV gag HIV gag SLYNTVATL epitope

We recommend reserving at least four bar codes for positive and negative controls.