Pacific Biosciences

The world's first single molecule,
real-time DNA sequencer

Overview

Pacific Biosciences introduces a revolutionary third generation DNA sequencing sytem incorporating novel single molecule sequencing with unprecedented real lengths to reveal new biological insights in real time.

SINGLE MOLECULE, REAL-TIME ANALYSIS

Single molecule, real-time (SMRT®) detection provides direct measurement of individual molecules, capturing multiple dimensions of data. Templates can be prepared for the PacBio RS without PCR amplification, resulting in more uniform sequence coverage across genomic regions regardless of GC content, facilitating the detection of minor variants in heterogeneous samples.

While observing single molecule sequencing by a highly processive strand-displacing DNA polymerase in real time, the system also records the kinetics of each nucleotide incorporation reaction, identifying base modifications of the native templates, such as DNA methylation.

LONGER READ LENGTHS

With read lengths in the thousands of bases, the PacBio RS can resolve both SNPs and large-scale structural rearrangements. Long reads increase understanding of disease heritability through haplotype phasing. Long reads also simplify and improve genomic assembly by reducing the number of contigs, and produce superior consensus accuracy compared to other technologies at the same depth of coverage.

FASTER TIME TO RESULTS

Read DNA at the speed of the polymerase in bases per second. With rapid sample preparation completed in 4-6 hours and short run times measured in minutes, you can obtain biologically meaningful answers within hours instead of a week or more. For data analysis, PacBio offers a robust suite of SMRT Analysis tools to speed up your time from data to insights.

FLEXIBILITY

Customize your experiments with granular, low cost consumables and adjustable run conditions. Multiple sequencing protocols provide maximum flexibility for a wide range of applications.

EASE OF USE

Prepare samples in a few hours without amplification. Monitor sequencing in real time, with feedback on the state of the PacBio RS, its contents, and your experiment through a touch-screen interface. Analyze data and view results in rich user interfaces built around industry standards. The entire workflow was designed with the user in mind - from sample preparation, to instrument use, to data analysis.

Applications

TARGETED RESEQUENCING

The PacBio RS is uniquely suited for variant validation due to high single molecule accuracy, extra long reads and granularity. Directly measure individual molecules with long reads to fully characterize genetic complexity, including rare SNPs, indels, structural variants, haplotypes and phasing.

Flexible experimental design supports rapid analyses of a few or hundreds of genes within hours. Single molecule resolution enables characterization of heterogeneous samples, including clinical samples (such as viral populations and tumor sections) and identification of variation invisible to population-based sequencing technologies.

DE NOVO ASSEMBLY

Hybrid assembly

Finish genomes and reduce contigs at a lower cost and with higher quality by combining long read PacBio® data with short read second generation sequencing data.

Solo de novo assembly

Assemble microbial genomes with PacBio data alone.

PATHOGEN IDENTIFICATION

Using rapid sample preparation and short run times, idetify and characterise pathogens with strain-level resolution for infectious outbreaks, biodefense, food safety and metagenomics.

FUTURE APPLICATIONS

Kinetic information

The unique ability of SMRT technology to observe kinetic information of individual molecules enables epigenetic studies to detect a wide variety of base modifications. SMRT technology has also been applied by researchers to directly observe transcription, RNA sequencing, translation and ligand-protein binding. PacBio plans to further develop and evaluate these applications for future release.

What is SMRT Technology?

The Pacific Bioscience SMRT technology harnesses the natural process of DNA replication, which is a highly efficient and accurate process. The enzyme responsible for replicating DNA, the DNA polymerase, attaches itself to a strand of DNA to be replicated, examines the individual base at the point it is attached, and then determines which of four nucleotides, is required to replicate that individual base. After determining which nucleotide is required, the polymerase incorporates that nucleotide into the growing strand that is being produced. After incorporation, the enzyme advances to the next base to be replicated and the process is repeated.

The SMRT technology enables the observation of this DNA synthesis as it occurs in real time.

To overcome the challenges inherent in observing an enzyme that is 15 nanometers (nm) in diameter running in real time, Pacific Biosciences developed three key innovations:

  • The SMRT Cell

  • Phospholinked nucleotides

  • The PacBio RS

Putting these three Innovations together allow researchers to sequence long reads of DNA in minutes.

The DNA polymerase is immobilized on the floor of the SMRT Cell in a Zero-mode Waveguide, or ZMW. Phospholinked nucleotides are introduced into the SMRT Cell from above and as the nucleotides diffuse through the bottom 30nm of each ZMW in the SMRT Cell, a small noise signal is generated. When the DNA polymerase encounters the nucleotide complementary to the next base in the template, it is incorporated into the growing DNA chain. During incorporation, the DNA polymerase holds the nucleotide for tens of milliseconds, orders of magnitude longer than the average diffusing nucleotide. While held by the polymerase, the fluorescent label emits colored light and the PacBio RS detects this as a flash of light whose color corresponds to the base identity, which is recorded. Following incorporation, the signal immediately returns to baseline and the process repeats, with the DNA polymerase continuing to incorporate multiple bases per second.

About Pacific Biosciences

Pacific Biosciences' mission is to transform the way humankind acquires, processes and interprets data from living systems through the design, development and commercialization of innovative tools for biological research.

The company has developed a novel approach to studying the synthesis and regulation of DNA, RNA and proteins. Combining recent advances in nanofabrication, biochemistry, molecular biology, surface chemistry and optics, Pacific Biosciences has created a powerful technology platform called single molecule, real-time, or SMRT®, technology.

SMRT technology enables real-time analysis of biomolecules with single molecule resolution, which has the potential to transform the understanding of biological systems by providing a window into these systems that has not previously been open for scientific study.

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