Roche's Genome Sequencer FLX System used for critical immunogenetic study

Oct 14 2009

A study published online today in the prestigious Nature Medicine journal reports that researchers at the Wisconsin National Primate Research Center have explored a new high-throughput method for decoding one of the most critical genomic regions for the immune system. In the study, they used ultra-deep sequencing with the Genome Sequencer FLX System from 454 Life Sciences, a Roche Company (SWX:RO) (SWX:ROG) (Pink Sheets: RHHBY), to perform rapid major histocompatibility complex (MHC) class I genotyping in macaques, a common model primate. The MHC is a gene-rich portion of the human and monkey genome that plays a critical role in the immune system. Robust genotyping methods are essential for studies of the T cell response, including research on autoimmune and infectious disease, transplantation, and vaccine development.

Genotyping efforts in nonhuman primates using existing technologies have frustrated research efforts for more than a decade due to the extreme complexity of this genomic region in macaques, even compared to humans. Importantly, the study demonstrates that the state-of-the-art 454 Sequencing System can dramatically improve upon traditional Sanger sequencing methods by enabling the discovery of new genotypes that had previously been missed. In the initial study, the Wisconsin researchers were able to characterize MHC genotypes in 48 individual monkeys in a single instrument run. They identified, on average, 22 distinct MHC class 1 transcript sequences in each monkey, demonstrating how much there is to uncover about immune response in these important model species.

“Comprehensive MHC genotyping has the potential to revolutionize the use of nonhuman primates in infectious disease and transplantation research and to guide functional immunology studies,” explained Dr. Roger Wiseman, lead author at the Wisconsin National Primate Research Center. “The abundance of long sequencing reads generated by the Genome Sequencer FLX System are critical for resolving closely related alleles, a truth that is becoming increasing clear as we begin to generate 500 base pair amplicons using the early-access GS FLX Titanium Series amplicon sequencing kits and software.”

The best known genes in the MHC region are the human leukocyte antigen (HLA) genes, which encode for the cell-surface proteins responsible for differentiating between self and non-self cells and other antigens. Understanding an individual’s HLA genotype is particularly important in matching donors and recipients in tissue transplantation since any cell displaying a non-self HLA type causes immunological rejection.

Perhaps the most exciting aspect of the study is its application to future immunologic genotyping efforts in humans. Not only does the new sequencing method offer much more comprehensive genotyping compared to existing technologies, it also may prove to be a cost effective solution. “Based on the yield from our macaques studies, we predict that HLA class I genotypes for thousands of individuals could be generated in a single Genome Sequencer FLX System run,” said Dr. David O’Connor, senior author, Associate Director of the Wisconsin National Primate Research Center and Assistant Professor at the University of Wisconsin-Madison. “We may soon be looking at a time where all donor samples in tissue registry programs are analyzed with the 454 Sequencing System.”

“This study shows the tremendous potential of 454 Sequencing Systems to fundamentally change the way we study the immune system and T cell response in human disease research,” said Michael Egholm, Chief Technology Officer and Vice President of R&D at 454 Life Sciences. “Rapid MHC genotyping and analysis of the VDJ antibody repertoire represent two critical ways in which the technology is opening new doors in the field of immunogenetics.”

Source Roche