Roche NimbleGen, BGI develop Major Histocompatibility Complex region capture technology

Nov 28 2011

Roche NimbleGen, Inc. and BGI, the world's largest genomic organization, announced that they have developed a Major Histocompatibility Complex (MHC) region capture technology based on NimbleGen SeqCap EZ Choice Library, a revolutionary process for the enrichment of the MHC region. This newly developed approach allows easy capture and enrichment of these highly repetitive regions and enables the generation of deep sequencing coverage of the human MHC region. This new sample preparation approach overcomes the limitations of traditional methods of PCR and genomic enrichment used for disease and drug research.

Major Histocompatibility Complex is a large cluster of genes found on the short arm of chromosome 6, covering a 3.6Mb region that includes 150 expressing genes. MHC has been shown to play a critical role in the development or progression of hundreds of diseases, including cancers, AIDs, diabetes, arteriosclerosis and leukemia. Given its integral function in the regulation of immune system, MHC has become a key target in drug research and development for a number of diseases.

MHC shows a high degree of polymorphism which complicates the studies of genes in this region, and its gene density (37 per Mb) is five times higher than the average gene density of the whole genome (7 per Mb). Because of it polymorphic nature, linkage disequilibrium, and inheritance of haplotype, MHC has been targeted for a wide range of research applications, including population evolution, paternity testing, HLA typing and organ transplant matching.

This new MHC region capture technology not only targets the traditional MHC region (3.37MB), its targets approximately 1.6Mb of the regions surrounding MHC, providing a total of 4.97Mb (chr6: 28477797-33448354) and includes 8 known haplotypes.

"This new technology enables targeted sequencing of 97% or more of the overall MHC region, and close to 100% coverage of the gene coding regions," said Hui Jiang, Technical Specialist at BGI. "The high accuracy of this new technology is demonstrated by a 99.42% concordance with traditional genotyping technologies.  But not only does this technology enable accurate genotyping of known SNPs, it provides the opportunity to discover novel SNPs."

"This MHC region capture technology had been optimized by advanced probe design and capturing methods with Roche NimbleGen, which greatly increases the coverage and capture efficiency of MHC region compared to all other approaches we have attempted in the past. Meanwhile, the pooling technology has been improved, which not only can efficiently capture multiple samples in a single reaction, but it also significantly reduces the cost. I believe the combination of this revolutionary capture technology with high-throughput sequencing technologies will help advance research and development of new medicines for human diseases." said Jiang.