Results From Two Multi-Site Collaborative Studies Highlight The Value Of 454 Sequencing Systems For Genotyping Applications

Main Category: HIV / AIDS
Article Date: 29 Jul 2010 - 0:00 PDT

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454 Life Sciences, a Roche Company (SWX:RO)(SWX:ROG)(Pink Sheets: RHHBY), has announced promising new results from a multi-site collaborative research study which used the company's Genome Sequencer FLX System to perform HIV drug-resistant mutation detection. The findings were outlined last month at the International HIV & Hepatitis Virus Drug Resistance Workshop in Dubrovnik, Croatia, and follow only weeks after the results from a similar multi-site research study, which used the company's sequencing technology for high-resolution HLA genotyping, were presented at the European Immunogenetics and Histocompatibility Conference in Florence, Italy.

Both double-blinded studies were performed by groups of collaborative research institutions with varying degrees of familiarity with the sequencing technology. The findings of each of the two studies include high-accuracy and concordance across sites.

The first study used the Genome Sequencer FLX System to perform ultra-deep targeted resequencing to detect rare HIV variants across the same samples at 11 research institutions. "The detection of the full range of mutant HIV variants in a sample, also known as viral quasispecies, is expected to be important for management of drug-resistant HIV-1 infections and the choice of combination antiretroviral therapy," explained Martin Daeumer, Study Lead and Laboratory Head of Infectious Disease at the Institute of Immunology and Genetics in Kaiserslautern Germany. "We found that the 454 System's deep sequencing method enabled the detection of both common viral variants and those undetected by standard population sequencing, with high intra- and inter-laboratory consistency." Specifically, the study results showed 100% concordance with standard Sanger sequencing for mutations with a Stanford Database score of ≥5.

The second study used the Genome Sequencer FLX System for HLA genotyping across eight research institutes. Accurate Human Leukocyte Antigen (HLA) genotyping is important in research of hematopoetic stem cell transplantation and a variety of autoimmune diseases, as well as some cancers and infectious diseases. "The abundance of long sequencing reads produced by 454 Sequencing Systems allowed unambiguous assignment of most HLA alleles in a much faster and more cost efficient manner than with traditional technologies," explained Henry Erlich, study author and Director of the Department of Human Genetics at Roche Molecular Systems. "Further studies will implement the GS FLX Titanium chemistry for higher throughput, longer sequence reads, and greater genomic coverage to provide even higher resolution HLA genotyping."

Based on the results of this study, 454 Life Sciences will introduce HLA primer sets for life science research later this year. The primers will be designed for use with the long read GS FLX Titanium reagent chemistry, which is employed on the GS FLX System and the recently launched GS Junior System.

"These highly robust findings support our belief that 454 Sequencing Systems are particularly well suited for detection of minority variants in mixed populations and unambiguous resolution of highly complex genomic regions," explained Christopher McLeod, President and CEO of 454 Life Sciences. "We are developing a menu of common assays, including specific analysis software, which will offer laboratories a streamlined solution for quickly and easily integrating targeted sequencing into their research. In addition, we are actively working to identify potential paths to bring 454 Sequencing Systems to the clinical market."

Source:
Roche

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