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Roche Introduces Next-Generation HLA Typing Solution for 454 Sequencing Systems

Roche
29 Mar 2011
bridget bridget
Laboratory Director

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454 Life Sciences, a Roche Company, announced today the launch and immediate availability of the new GS GType HLA Primer Sets for high- and medium-resolution genotyping of class I and class II loci of the Human Leukocyte Antigen (HLA) genes. The primer sets are designed for use with the company’s benchtop GS Junior and GS FLX next-generation sequencing systems – enabling high-resolution typing and unambiguous allele assignment in a single run.

The solution represents a major advance in speed and quality of characterization of this immunologically important and highly variable region of the human genome. The kits are the first in a series of research assays in the areas of immunogenetics, infectious disease, and cancer to be launched for use with 454 Sequencing Systems, allowing researchers to easily integrate the platforms into application-specific laboratory workflows.

The HLA genes encode for the immune system proteins that recognize foreign cells and other antigens. Accurate characterization of an individual’s HLA type is important for research in tissue transplantation matching, while variations in these genes have known association with a wide variety of autoimmune diseases, infectious diseases, and some cancers. The HLA genes present a challenge for genotyping due to the highly polymorphic nature of this region of the human genome.

Traditional sequence-based typing using Sanger capillary electrophoresis technology is unable to resolve ambiguities and set phase without requiring multiple iterations, interspersed with significant manual analysis of the data, and often the use of multiple technologies. The unique long, clonal reads provided by 454 Sequencing Systems enable straightforward high-resolution HLA typing of multiple samples at a time and, in many cases, achieve unambiguous allele identification within a single sequencing run. Sequence output is compatible with third party HLA genotyping software tools – offering researchers a complete solution from DNA to genotype assignment.

The GS GType HLA Primer Sets are the result of an extensive multi-site study, published this month in the journal Tissue Antigens 1. “We have sequenced thousands of samples and find the >99% concordance rate, increased throughput and significant reduction of ambiguity is far superior using the Roche GS FLX System over Sanger-based approaches,” said Elizabeth Trachtenberg, Ph.D, study author and Director of the HLA/Immunogenetics Laboratory at the Children’s Hospital & Research Center Oakland. “Using this approach, we can obtain a high-resolution allele assignment in approximately one-third the time necessary using Sanger-based methods.”

“454 Sequencing Systems offer a major advance for high-resolution, high-throughput HLA typing,” explained Henry Erlich, Ph.D., senior study author and Director of the Department of Human Genetics at Roche Molecular Systems. “The ability to quickly achieve such high accuracy and resolution will have a significant impact on research and, ultimately, on clinical application of HLA typing.”

For more information on 454 Sequencing Systems, visit the company article page.

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GS Junior System

The power of next-gen sequencing in your hands. The GS Junior System brings the power of 454 Sequencing Systems directly to the laboratory benchtop. Get comprehensive genome coverage with long 400 bp sequencing reads and quickly proceed from DNA to discovery with fast sequencing runs and straightforward data analysis on the attendant computer.GS Junior System Features: Powered by proven technology: Uses GS Junior Titanium chemistry to deliver high-quality, bioinformatics-friendly, long read data Fits in your lab: Small instrument size, along with low entry and operating costs, enables labs with limited budget and infrastructure to take advantage of next gen sequencing Easy to use: Manageable data size allows processing and analysis right on the attendant computer without the need for specialized computing or network infrastructures Point-and-click data analysis: Includes the GS Data Analysis Software for de novo assembly, reference mapping and amplicon variant analysis Applications: Amplicon Sequencing: Targeted sequencing of 10's - 100's of samples and loci Sequence Capture: Targeted sequencing of custom array regions Whole Genome Sequencing: De novo sequencing and resequencing of microbial organisms (bacteria, fungi, viruses) Metagenomics: Characterization of complex environmental samples; pathogen discovery Transcriptome Sequencing: Full-length sequencing and de novo assembly of transcripts

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GS FLX+ System

Roche

Now delivering sequencing reads up to 1,000 bp in length! The GS FLX+ System features the unique combination of long reads, exceptional accuracy and high-throughput, making the system well suited for larger genomic projects. The GS FLX System has been at the heart of key breakthrough genomic discoveries and over 1,000 peer-reviewed publications to date.Advancements in sequencing chemistry, instrumentation and software offer the latest improvements in GS FLX System performance, with read lengths up to 1 kb. Available as an on-site instrument upgrade or new instrument, the GS FLX+ System is designed for use with both the new long-read Sequencing Kit XL+ and existing Sequencing Kit XLR70.GS FLX+ System Features: True capillary sequencing-like read lengths: Continuous development of the GS FLX Titanium chemistry now offers read lengths up to 1 kb Flexible sequencing formats: Broad selection of gaskets and Multiplex Identifiers (MIDs) enables efficient use of sequencing runs Point-and-click data analysis: Included GS Data Analysis Software for de novo assembly, reference mapping and amplicon variant analysis. Applications: Whole Genome Sequencing: De novo sequencing of large, complex organisms or multiple bacterial genomes in a single run Transcriptome Sequencing: Full-length de novo sequencing and assembly of complex organisms Amplicon Sequencing: High-throughput sequencing of 100s to 1,000s of samples and loci Sequence Capture: Targeted resequencing of whole exomes or large capture regions Metagenomics: Characterization of complex environmental samples; pathogen discovery

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