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



Service CFAR Academic List Unit
Kapa $20.00 $24.20 $36.20 sample
Pico Green $5.00 $6.05 $9.05 sample
TapeStation $15.00 $18.15 $27.15 sample
miSeq-300 $1,785.00 $2,159.85 $3,230.85 lane
miSeq-500 $2,040.00 $2,468.40 $3,692.40 lane
miSeq-micro-300 $1,465.00 $1,772.65 $2,651.65 lane
miSeq-nano-300 $1,135.00 $1,373.35 $2,054.35 lane
miSeq-nano-500 $1,270.00 $1,536.70 $2,298.70 lane
miSeq-v3_150 $1,615.00 $1,954.15 $2,293.15 lane
miSeq-v3_600 $2,370.00 $2,867.70 $4,489.70 lane
Hour-Lab $115.00 $139.15 $208.15 hour
Analysis $205.00 $248.05 $371.05 instance
Sample prep (purify DNA, amplify) $22.00 $26.62 $39.82 per sample
454 Junior Sequencing Run $2,715.58 $2,385.85 $4,928.78 per run
Preparation for samples for integration site analysis $249.00 $301.29 $451.94 per sample
Integration site work up, gene therapy $619.63 $749.75 $1,124.63 per sample
Programmer Time $90.00 $108.90 $162.35 per hour
Bioinformatics Analyst Time $150.00 $181.50 $271.50 per hour

Penn CFAR Member pricing is available to faculty and lab personnel at the University of Pennsylvania, Children's Hospital of Philadelphia, and the Wistar Institute.