454 Sequencing System Opens New Avenue in Prostate Cancer Research

Using the Genome Sequencer FLX system from 454 Life Sciences, a Roche company, investigators have identified a number of genetic variations potentially linked to prostate, breast, and colon cancers within a previously identified region of the human genome called 8q24. Researchers from the National Cancer Institute in Bethesda, Maryland (USA) re-sequenced a total of 85 individuals representing case and controls for prostate and colon cancers. This included 39 individuals with advanced prostate cancer and 40 individuals from the National Cancer Institute’s Prostate, Lung, Colorectal, and Ovarian Screening Trial. Additionally, 6 individuals from the public HapMap project were sequenced to provide quality control. The study, entitled “Comprehensive Resequence Analysis of a 136kb region of Human Chromosome 8q24 Associated with Prostate and Colon Cancers”, appears on August 14th in the journal Human Genetics.

Resequencing the 136 kilobase 8q24 region from the 3 billion base human genome, the researchers identified over 1000 genetic variations in the 85 individuals. A total of 442 novel single nucleotide polymorphisms (SNP’s) were identified. Demonstrating the data quality achieved using the technology of the 454 Sequencing System, a representative subset of the data showed a greater than 99% concordance with previously published results. The study’s findings will be used to further additional studies to identify possible genetic variations that lead to disease.

“The project that supported this publication is one of many exciting breakthrough applications of the Genome Sequencer system,” said Chris McLeod, CEO of 454 Life Sciences. “The vision at 454 is to make the resequencing of individual human genomes routine. To see the platform being used to study over 80 individuals for such an important disease is definitely a step in that direction. As our sequencing read lengths increase and our workflow becomes more streamlined, we envision a complete transformation for the genotyping market.”

One of the major goals in whole genome genotyping studies is to identify those genetic variations that contribute to a phenotype. There are a few commercially available technologies that can readily identify regions of the human genome that may have strong associations with a disease, but these technologies usually miss the causative genetic variation. Using next generation sequencing now allows researchers to quickly and economically discover nearly all the genetic variations within those regions with the goal of identifying the causative genetic variation.