Researchers Successfully Used the 454 Sequencing System for Sensitive Detection of HIV Tropism

454 Life Sciences, a Roche company, announced today that a team of researchers from the BC Centre of Excellence in HIV/AIDS and the University of British Columbia, Canada have used the Genome Sequencer FLX system to monitor low frequency HIV variants from human samples in a recent study. The preliminarily results of the study were presented by Dr. Richard Harrigan, the Centre’s Director of Research Labs at the HIV DART 2008 conference in Puerto Rico in a presentation entitled “Quantification of HIV Tropism by Deep Sequencing Shows a Broad Distribution of X4 Variants in Clinical Samples Associated with Virological Outcome.”

The background of this research study is that correct determination of “HIV tropism” is critical for the administration of a new class of drugs called CCR5 antagonists used for the treatment of AIDS. HIV tropism refers to the type of cell the HIV virus infects, as determined by so-called co-receptors that the virus employs for entry into the cell. Determining the co-receptor that a HIV strain uses, either CCR5, CXCR4 or a combination of both, is a critical component of monitoring and treating HIV.

The preliminary results of the study found that conventional genotyping methods lack sufficient sensitivity for detection of the CXCR4 variant which is a contraindication for adminstering CCR5 antagonists. By using deep sequencing with the Genome Sequencer FLX system, the researchers were able to quantify low-frequency variants associated with poor response to CCR5 antagonists and accurately determine HIV tropism across all individuals’ samples.

"The sensitivity of the Genome Sequencer FLX platform allowed us to monitor HIV sequence variation from 48 or 96 individuals´ samples simultaneously, and still have far greater ability to spot minority variants than using standard approaches,” explained Dr. Richard Harrigan. “The result was the ability to detect HIV tropism accurately in all samples from this study. Standard methods were missing up to 35 percent of the answers. This has important implications for therapy monitoring. The fact that the Genome Sequencer FLX system gives a quantitative measure of sequence variance within a sample is a bonus".

“The sequencing technology of 454 Life Sciences is a critical tool for research on viral diseases and their possible treatment. The system shows potential for sensitive profiling of viral populations for enhanced monitoring and for the development of more personalized therapies,” said Christopher McLeod, President and CEO of 454 Life Sciences. “We believe that, in the near future, the 454 Sequencing system will transform the way HIV is monitored and treated.”

454 Life Sciences, a center of excellence of Roche Applied Science, develops and commercializes the innovative 454 Sequencing system for ultra-high-throughput DNA sequencing. Specific applications include de novo sequencing and re-sequencing of genomes, metagenomics, RNA analysis, and targeted sequencing of DNA regions of interest. The hallmarks of the 454 Sequencing system are its simple, unbiased sample preparation and long, highly accurate sequence reads, including paired-end reads. The technology of the 454 Sequencing system has enabled hundreds of peer-reviewed studies in diverse research fields, such as cancer and infectious disease research, drug discovery, marine biology, anthropology, paleontology and many more.

The 454 GS FLX is sold for life science research use only. The 454 Genome Sequencer FLX is intended only for use in basic or applied laboratory research, and is not intended for use in human diagnostics. Roche Diagnostics does not condone any use of the 454 Genome Sequencer FLX other than basic or applied laboratory research, and Roche Diagnostics will not support any other use.

454, 454 SEQUENCING, 454 LIFE SCIENCES, and GS FLX TITANIUM are trademarks of Roche.