July 2, 2012

Nature Biotechnology Publications Showcase Value of PacBio RS in De Novo Genome Assembly

Scientists Use PacBio Long Reads to Simplify and Automate the Genome

Assembly Process, Dramatically Reduce Contig Numbers, and Resolve

Structural Variation


Two papers in Nature Biotechnology, both published online on July

1, 2012 highlight the unique value for de novo genome assembly

provided by the PacBio® RS High Resolution Genetic

Analyzer from Pacific Biosciences of California, Inc. (NASDAQ:PACB).

Due to the inherent limitations of commonly used short-read sequencing

technologies, the genomes of very few species have been completely

sequenced, or “finished.” PacBio’s single molecule, real-time (SMRT®)

technology offers very long reads that reduce the number of contiguous

sequences, or contigs, to simplify and improve genome assembly. These

multi-kilobase reads allow scientists to sequence through long repeat

regions and to identify structural variation, which are common in

genomes but not possible to resolve completely with short-read

platforms. As a result, PacBio long reads can lead to final assemblies

that match—and in some cases even exceed—the quality that previously

counted as “finished,” approaching the gold standard of a perfect genome.

In the publication from Koren et al., titled “Hybrid error correction

and de novo assembly of single-molecule sequencing reads,” the authors

demonstrate a new pipeline for assembly of the parrot genome. Using

PacBio long reads in combination with high-accuracy short reads and an

updated version of Celera Assembler, they assembled for the first time

regulatory regions of genes involved in vocal learning circuits. The

hybrid reads represent the most complete assembled bird genome now


“Repetitive regions are the biggest impediment to all assembly

algorithms and sequencing technologies as they introduce ambiguity in

the reconstruction of the genome,” said Sergey Koren, Ph.D., Scientist

of Bioinformatics at the National Biodefense Analysis and

Countermeasures Center. “Using the long reads we have access to longer

sequences, which increases the probability of spanning a repeat and

leads to better assemblies at lower depths than short reads.”

A separate publication from Bashir et al., titled “A hybrid approach for

the automated finishing of bacterial genomes,” describes combining

contigs from second-generation sequencing technologies with PacBio

sequence data for the cholera strain responsible for the 2010 Haitian

outbreak. The authors show that their hybrid assembly resolved complex

regions with several repeats and suggest that the approach offers a

solution for “rapid identification and assembly of full microbial


“The publication of these two studies is evidence of how our long-read

technology is emerging as the gold standard for finishing genome

assemblies and identifying, annotating and deciphering genomic

structure,” said Mike Hunkapiller, President and CEO at Pacific

Biosciences. “Moreover, investigators are finding creative ways to take

advantage of the unique benefits provided by our SMRT sequencing and

enabling scientific applications that are simply not possible with

short-read sequencing platforms.”

The Nature Biotechnology publication details are as follows:

  • “Hybrid error correction and de novo assembly of single-molecule

    sequencing reads.” Sergey Koren et al., National Biodefense Analysis

    and Countermeasures Center.

  • “A hybrid approach for the automated finishing of bacterial genomes.”

    Ali Bashir et al., Pacific Biosciences and Mount Sinai School of


For more information on de novo genome assembly with the PacBio®

RS, please visit our website at

About Pacific Biosciences

Pacific Biosciences of California, Inc. (NASDAQ: PACB) offers the PacBio®

RS, a high resolution genetic analyzer, to help scientists solve

genetically complex problems. Based on its novel single molecule,

real-time (SMRT®) technology, the company’s products enable:

targeted sequencing to more comprehensively characterize genetic

variations; de novo genome assembly to more fully identify,

annotate and decipher genomic structures; and DNA base modification

identification to help characterize epigenetic regulation and DNA

damage. By providing access to genetic information that was previously

inaccessible, Pacific Biosciences enables scientists to increase their

understanding of biological systems.

Forward-Looking Statements

This press release contains forward-looking statements. Forward-looking

statements may contain words such as “believe,” “may,” “estimate,”

“anticipate,” “continue,” “intend,” “expect,” “plan,” the negative of

these terms, or other similar expressions, and include the assumptions

that underlie such statements. Such statements include, but are not

limited to, statements regarding the Company’s SMRT technology. These

statements are subject to known and unknown risks and uncertainties that

could cause actual results to differ materially from those expressed or

implied by such statements, including but not limited to risks discussed

from time to time in documents Pacific Biosciences of California, Inc.

has filed with the Securities and Exchange Commission, including the

risks identified under the section captioned “Risk Factors” in its

recently filed Quarterly Report on Form 10-Q. All forward-looking

statements are based on estimates, projections and assumptions as of the

date hereof. Pacific Biosciences undertakes no obligation to update any

forward-looking statements.

For Pacific BiosciencesNicole Litchfield, 415-793-6468 (Media)

BiosciencesTrevin Rard, 650-521-8450 (Investors)

Source: Pacific Biosciences of California, Inc.

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