Pacific Biosciences of California, Inc., (Nasdaq:PACB) provider of
the PacBio® RS II, today announced the release of a software
upgrade for its Single Molecule, Real-Time (SMRT®) DNA Sequencing
platform. SMRT Analysis 2.2 provides enhanced functionality to
support two additional applications that uniquely benefit from the
company's long-read sequencing technology: Iso-Seq™ full-length
transcript/isoform sequencing, and human leukocyte antigen (HLA)
haplotype phasing.
The study of mRNA transcript isoforms has been challenging due
to the short read lengths of other sequencing technologies. Long
PacBio reads enable full-length transcript sequencing, as well as
the identification of alternatively spliced forms of a gene. As a
result, new genes and isoforms are accessible for study.
For example, Steve Quakeand Thomas Südhof,Professors at Stanford
University and Investigators with the Howard Hughes Medical
Institute, together with colleagues, used SMRT Sequencing to
characterize the genes encoding neurexins, which are involved in
the formation of connections between cells in the human braini.
Because of the high number of different splice isoforms, these
genes have been extremely difficult to study and, despite extensive
efforts, the full extent of neurexin alternative splicing remained
unclear. Using PacBio long-read sequencing, the researchers
identified hundreds of different isoforms in the neurexin gene
family, highlighting a staggering complexity of these gene products
and providing more insight to the notion that neurexins function as
recognition molecules that contribute to the specification of cell
connections in the brain.
The Iso-Seq application can also be used for transcriptome-wide
studies, improving the ability to annotate genes in reference
genomes. Long sequence reads spanning full-length gene
transcripts will eliminate the need for an RNA-seq assembly step,
providing more complete gene models and more comprehensive
annotation of transcribed genes.
Michael Snyder's lab at Stanford University demonstrated
the utility of PacBio long-read sequencing for assessing
transcribed regions across the human genome in a paperii last
October. Dr. Snyder commented: "Full length transcriptome
sequencing allows the analysis of complete transcriptomes including
the deciphering of complex transcripts and the discovering of
new ones. PacBio sequencing works remarkably well for this."
The second new application is HLA haplotype phasing. The HLA
loci are a group of genes critical to immune system
function. In humans, the HLA genes are extraordinarily
polymorphic. Several thousand alleles have been described and the
number of new alleles continues to increase. HLA allele-specific
genotyping is critical for autoimmune disease-association studies,
drug hypersensitivity research and other applications. Accurate
phasing of HLA polymorphisms has previously required several
experiments at great expense. The long reads provided by PacBio
sequencing are ideally suited for accurate allele-level genotyping
with unambiguous allele phasing.
PacBio's SMRT Analysis 2.2 generates consensus sequences that
can be input into third-party software for HLA analysis. This data
has successfully been used with the Conexio Genomics (Perth,
Australia) Assign MPS sequence analysis software.
"PacBio's analysis pipeline independently generates the
consensus sequence of each allele in a heterozygous sample,
including non-coding regions," said David Sayer, Chief Executive
Officer of Conexio Genomics. "When analyzed in our sequence
analysis software, this data results in a completely phased,
immutable HLA genotype. The analysis is simple and rapid."
"The SMRT Analysis 2.2 upgrade streamlines two important
applications that are uniquely enabled by our robust long-read
sequencing technology," said Michael Hunkapiller, President and CEO
of Pacific Biosciences. "We are excited about the trajectory that
has unfolded with each increase in the performance of the PacBio RS
II system, and look forward to seeing what novel insights the
research community will uncover with these new applications."
The new SMRT Analysis software upgrade is available for download
from Pacific Biosciences' DevNet website. To access the software,
data, and documentation, visit www.pacbiodevnet.com.
For more information on the new SMRT Analysis software and the
PacBio RS II, please visit www.pacificbiosciences.com.
About the PacBio RS II and SMRT Sequencing
Pacific Biosciences' Single Molecule, Real-Time (SMRT)
Sequencing technology achieves the industry's longest read lengths,
highest consensus accuracyiii,iv and the least degree of bias.v
These characteristics, combined with the ability to detect many
types of DNA base modifications (e.g., methylation) as part of the
sequencing process, make the PacBio RS II an essential tool for
many scientists for studying genetic and genomic variation. The
PacBio platform is being used as the sequencing solution to address
a growing number of complex medical, agricultural and industrial
problems.
About Pacific Biosciences
Pacific Biosciences of California, Inc. (Nasdaq:PACB) offers the
PacBio RS II DNA Sequencing System 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 information that was previously
inaccessible, Pacific Biosciences enables scientists to increase
their understanding of biological systems.
i Treutlein et al., "Cartography of neurexin alternative
splicing mapped by single-molecule long-read mRNA sequencing."
PNAS, 10.1073/pnas.1403244111 (2014).
ii Sharon et al., "A single-molecule long-read survey of the
human transcriptome," Nature Biotechnology 31, 1009–1014
(2013).
iii Koren et al., "Reducing assembly complexity of microbial
genomes with single-molecule sequencing." Genome Biology, 14:R10.1
(2013).
iv Chin et al., "Nonhybrid, finished microbial genome assemblies
from long-read SMRT sequencing data." Nature Methods, 10; 563-569
(2013).
v Ross et al. Characterizing and measuring bias in sequence
data. Genome Biol 14: R51 (2013).
CONTACT: For Pacific Biosciences:
Media:
Nicole Litchfield
For Pacific Biosciences
415.793.6468
nicole@bioscribe.com
Investors:
Trevin Rard
Pacific Biosciences
650.521.8450
ir@pacificbiosciences.com
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