Researchers at the Wisconsin National Primate Research Center have explored a high-throughput method for decoding one of the most critical genomic regions for the immune system.
In this study, which was published online in the Nature Medicine journal, the researchers used ultra-deep sequencing with the Genome Sequencer FLX System from 454 Life Sciences, a Roche company, to perform rapid major histocompatibility complex (MHC) class I genotyping in macaques (common-model primates).
The MHC is a gene-rich portion of the human and monkey genome that plays a critical role in the immune system.
Genotyping methods are essential for studies of the T cell response, including research on autoimmune and infectious disease, transplantation and vaccine development.
The study demonstrates that the 454 sequencing system can 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 characterise 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.
'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,' said Dr Roger Wiseman, lead author at the Wisconsin National Primate Research Center.
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 important in matching donors and recipients in tissue transplantation, since any cell displaying a non-self HLA type causes immunological rejection.
The study applies to future immunologic genotyping efforts in humans.
'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,' said Michael Egholm, chief technology officer and vice-president of research and development at 454 Life Sciences.
