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 characterizing complex populations such as HIV and SIV, HBV/HCV, and sites of retroviral DNA integration.

The Viral/Molecular Core is now offering Illumina sequencing as a service. In each case, amplicons will be generated from samples of interest, then sample sequences determined. Sequences are subject to stringent quality control algorithim and provided to users in fasta format. Bioinformatic analysis is available on a fee-for-service basis. 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 viral genomes
  3. Sequencing of sites of retroviral DNA integration
  4. Programmer time for data analysis


The Core provides support for each of these areas through the expertise of Dr. Frederic 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 Aubrey Bailey.

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:
Aubrey Bailey
Viral and Molecular Core


Deep sequencing of HIV-1 viral genomes

The goal of these studies is to obtain deep sequence information on specific regions of a virus of interest. Up to 46 samples can be analyzed per sequence run, though fewer samples may be run if specific applications require greater depth of sequencing. Typical applications might be tracking development of drug resistant or immune escape variants over time. Bar coded primers are used to amplify the same region over many samples (PMID:17576693). Amplicons are pooled, and the subjected to 454/Roche pyrosequencing. Sequence reads are then quality filtered, separated based on bar codes into the original samples. Initial sequence work up, analysis, and storage are included in the price of the sequencing run. Analysis may include quantification of diversity within each sample, or tracking one or several user-defined sequences across the sequence population; additional forms of basic analysis may be included in the base cost upon discussion with Core personnel. More sophisticated analysis can be purchased via programmer time (item 4, above).

Examples of analysis can be found at PMID:18614863, PMID:17576693, PMID:20375170.