SMRT? (Single Molecule Real Time) Biology is the application of Pacific Biosciences’ transformative detection platform to the real-time monitoring of biological processes at single molecule resolution and in specific, relevant contexts. This revolutionary strategy enables scientists to obtain a more complete characterization of the molecular interactions that define cellular processes. Essential to SMRT Biology are advanced informatics techniques that can integrate these high-dimensional data and enable the creation of richly informative models depicting interdependent relationships in living systems.
“Solving the puzzle of complex diseases, from obesity to cancer, will require a holistic understanding of the interplay between factors such as genetics, diet, infectious agents, environment, behavior, and social structures.”
Elias Zerhouni
The NIH Roadmap, Science 302:63-64 (2003).
Why is it Important?
Complex biological systems are dynamic, highly modular, and adaptive systems able to reconfigure themselves as conditions demand. The scientific community is increasingly recognizing that multiple data sources (e.g., DNA, RNA, protein and metabolite levels, etc.) and sophisticated computational approaches that integrate diverse data are required to uncover the hierarchy of molecular, cellular, and tissue based networks defining complex physiological and disease states.
While a significant technological revolution in biology has led to this realization, limitations in the available technologies have hampered the ability to embrace this scale of complexity. In order to fully realize the promise of personalized medicine, scientists require a means to obtain a comprehensive understanding of the fundamental building blocks of biological systems.(Figure 17)
Figure 17.
Pacific Biosciences’ Solution
Pacific Biosciences has developed a transformative technology platform for real-time detection of biological events at single molecule resolution. The first commercial application for this platform is DNA sequencing (available in 2010). Pacific Biosciences has begun expanding internal research programs and developing collaborations for additional ‘SMRT Biology’ applications and bioinformatics tools that will allow scientists to acquire new, fundamental knowledge about the molecular dynamics of life. These include simpler and more direct solutions for RNA sequencing, methylation sequencing, and even the largely uncharted real-time observation of protein translation.
DNA Sequencing
SMRT? DNA Sequencing offers very long reads, ultra-fast cycle times, and the flexibility to cost-effectively perform small or large projects. Because the SMRT DNA sequencing system provides temporal information about every base incorporation event, it can measure the kinetics of the enzyme independently for each base in a DNA sequence. The kinetics of incorporation are sensitive to, for example, the methylation status of the DNA template being sequenced. SMRT sequencing will unify the formerly separate applications of real-time, single-molecule DNA sequencing and methylation sequencing. This creates the potential to visualize methylation status and other epigenomic markers as a by-product of ordinary DNA sequencing with no change in sample preparation or run conditions. SMRT sequencing will unify the formerly separate applications of DNA sequencing and methylation sequencing. In addition, elimination of the bisulfite conversion step will save time and money as well as avoid the deleterious effects of conversion.
Read more about SMRT Sequencing for Resequencing and DeNovo applications
RNA Sequencing
Currently, the majority of nucleic acid sequencing is based on DNA, requiring RNA to be converted to cDNA prior to analysis. This can result in conversion bias, generation of spurious chimeras, and additional time and cost. Through the use of an RNA-dependent polymerase (such as a reverse transcriptase), RNA can be sequenced directly using the SMRT sequencing paradigm. Through the use of an RNA-dependent polymerase (such as a reverse transcriptase), RNA can be sequenced directly using the SMRT? sequencing. With the long readlength inherent in SMRT sequencing and no conversion bias, the polynucleotide structure of individual transcripts will be available for the first time without the need to rely on paired ends and inferences made across many molecules.
Other Applications of SMRT Biology
We expect numerous other applications of SMRT Biology will emerge. Pacific Biosciences is incubating academic research in other methods that will benefit from the SMRT Biology detection platform. For example, the machinery of protein synthesis, the ribosome, is another molecular apparatus that works from a template and performs cyclical additions based on nucleic acid sequence. By using fluorescent-labeled tRNAs, ribosomes can be observed in the same way polymerases are in SMRT DNA sequencing. By using fluorescent-labeled tRNAs, ribosomes can be observed in the same way polymerases are in SMRT DNA sequencing. As a piece of RNA is translated by the ribosome, the identity of the synthesized protein can be established by observing the sequence of tRNAs delivering amino acids to the ribosome. This will allow direct observation of protein synthesis over the entire proteome, without dependence on mRNA expression profiles.
In addition, because the system tracks temporal information, such studies will reveal the time-dependence of regulatory processes such as siRNA binding. By making the SMRT Biology technology available to the academic community, we expect numerous other uses of the system will be revealed. We encourage researchers to contact us to gain access to the SMRT Biology platform.
SMRT Informatics
The SMRT Biology platform will generate unprecedented scales and diversity of data on a daily basis. For example, from a single blood sample, scientists could produce a complete genome sequence, as well as a complete characterization of the RNA transcriptome, methylation patterns, and an assessment of the translational efficiencies in each individual cell type that can be isolated from blood. This will produce tens to hundreds of terabytes of data per sample.
Pacific Biosciences is developing an environment in which scientists can seamlessly integrate multiple data types from multiple sources and deploy advanced bioinformatics methods to elucidate the complexity of living systems. Therefore, we are committed to providing users with access to the right types of high-performance computing (HPC) environments to not only store and organize the data, but to enable analyses of the data on multiple different levels, from assembly of genomes to the construction of predictive models of disease. For example, we will provide cloud-based computing as one type of HPC service that leverages massive-scale compute environments in order to meet intense data storage and computational needs.
These informatics solutions will be designed to efficiently represent that magnitude of data and make it accessible not only to high-end informatics researchers, but also to biologists, clinicians and even patients. We believe this integration of real time biological data at single molecule resolution will be instrumental to in making personalized medicine a reality.
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