The DNA sequencing we do at engencore with the Roche 454 covers a wide range of applications in various fields of biology. Our system provides a great combination of accuracy, read length, and throughput.
As more traditional pharmaceutical firms move from chemical compounds to ones made from biological material, the importance of genomic sequencing rises. Genome sequencing can potentially create a new class of therapeutics in the form of personalized medicine and eliminate certain side effects of current therapeutics. Genetic sequencing also has significant applications in diagnostics where more accurate diagnostic tests can be developed at a lower cost through reducing R&D time and lessening the amount of investment needed for a diagnostic test.
Cancer research and diagnostics is perhaps the fastest-growing application for genomic sequencing targets. Through initiatives like the Cancer Genome Project, scientists hope to classify every cancer according to their molecular markers and make this information available to therapeutic and diagnostic researchers. The Roche 454 platform is ideal for this type of research, as its applications include somatic variation detection, transcriptome sequencing, epigenetic studies, tumor virus detection and small RNA.
Characterize and quantify the viral population within an infected individual with Ultra-Deep 454 Sequencing. The Genome Sequencer FLX System enables accurate and quantitative assessment of HIV quasi-species through the sequencing of target genes (ex. protease and reverse transcriptase genes). Sequencing hundreds of thousands of individual DNA molecules simultaneously, the 454 System detects rare genetic variants constituting as little as 1% of the population, levels far deeper than those of traditional sequencing methods. Furthermore, long reads elucidate haplotypes within each amplicon.
The Earth’s surface is ¾ water. A recent study has shown that for every teaspoon of sea water, there are 10^9 viruses making them perhaps the most abundant life form on Earth. Understanding the diversity and importance in transfer of genetic material among different bacterial species is being facilitated by the Roche/454 FLX platform (High abundance of viruses found in aquatic environments; Bergh O, Børsheim KY, Bratbak G, Heldal M.; Nature 1989 Aug 10;340(6233):467-8)
The Roche 454 platform’s ultra-high throughput and multiplexing capabilities afford a tremendous flexibility in experimental design for the sequencing of small genomes, viruses, plasmids, or mitochondria. Up to hundreds of sequences on a single run, long reads typically enable the assembly of shotgun sequence data with a minimal number of contigs.
For each human on Earth, there are an estimated 10^20 bacteria of which most of these (10^14) live in our digestive system. The Roche/454 platform has allowed and unprecendented insight into the composition of the complex bacterial communities that live in and around us.
(Whitman WB, Coleman DC, Wiebe WJ, Prokaryotes: the unseen majority., Proceedings of the National Academy of Sciences (USA), 95(12), 6578-83, 9 1998)
Somatic Variation Detection
Long reads and ability to sequence from single DNA molecules enables straightforward identification of low frequency somatic mutations. Effectively detect the spectrum of variations in specific disease-associated regions or genes by sequencing PCR products, cDNA libraries, or DNA fragments captured with NimbleGen’s Sequence Capture array.
Warfarin is the generic name of an anticoagulant drug which takes many months in order to achieve correct patient dosage. The 454 can be instrumental for targeted therapeutics research to help predict drug safety and effectiveness.
Environmental samples can provide a rich survey of genomic diversity. Shotgun Sanger sequencing and pyrosequencing are cutting-edge techniques designed to procure unbiased samples of all genes from the members of the sequenced communities. The Roche 454 platform is ideal for this purpose because it uses long reads and barcoded tabs to analyze the various microbial species in different environmental conditions and to compare the results against DNA or protein databases.
Plant materials are used in food, clothing, building materials, energy production and pharmaceuticals. The 454 can be used to discover biomarkers of plant species under critical conditions such as temperature, disease and drought. It can be used to study factors affecting growth, for example, in finding essential functional genomic mechanisms of synthesis of plant material grown under stress. The Roche 454 platform is a popular sequencing tool for researchers because it takes long reads with a high degree of accuracy and outputs high-quality data.
Biomass / Bio-fuel
Biomass, including biofuels, biomaterials, and transgenic proteins, involves taking DNA from organic life forms such as grasses, weeds, and trees and using them as the building block for growth.
The market for biomasses is predicted to significantly grow in coming years as sustainability assumes a greater role for businesses and policy makers. There are genes and their enzymes which are key in the production of biofuels. Finding metagenomic sequences of these key genes and enzymes is much more efficient using the 454. Whether looking at the hindgut of a termite or the characteristics of cellulosic material, the extensive data produced by the 454 provide answers.