Roche 454 Life Sciences has announced that a team of researchers have used the Genome Sequencer FLX system to monitor low frequency HIV variants from human samples in a recent study.
Researchers were from the BC Centre of Excellence in HIV/Aids and the University of British Columbia, Canada.
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 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 administering 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 individual 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,' said 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 per cent 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 system shows potential for sensitive profiling of viral populations for enhanced monitoring and for the development of more personalised therapies,' said Christopher McLeod, president and chief executive officer of 454 Life Sciences.
