New Publications Highlight Utility of Single Molecule, Real-Time Sequencing for Structural Variation Detection, Haplotype Reconstruction and De Novo Human Genome Assembly
Monday, July 13, 2015
MENLO PARK, Calif., July 13, 2015 (GLOBE NEWSWIRE) — A number of new scientific publications demonstrate the growing momentum for using Single Molecule, Real-Time (SMRT®) Sequencing to capture genetic variants that other technologies miss, according to Pacific Biosciences of California, Inc., (Nasdaq:PACB) provider of the PacBio® RS II Sequencing System. This has been demonstrated through the generation of several high-quality de novo human genome assemblies, which include a more complete view of structural variation. Together, they indicate the increasingly common use of SMRT Sequencing to interrogate human genomes, resolve haplotypes, detect structural variants, and fill gaps that have been intractable with other
The new publications, which highlight the cost and quality benefits of PacBio whole genome sequencing at both low and high coverage, appear in high-impact scientific journals including Nature Biotechnology, Nature Methods, and BMC Genomics. The papers also contribute to the growing suite of community-developed analysis tools for SMRT sequence data.
The publication in Nature Biotechnology, from scientists at the University of Maryland and the National Biodefense Analysis and Countermeasures Center (NBACC), includes a human genome assembly as one of the tests for their new MinHash Alignment Process (MHAP), an algorithm optimized for long reads and designed to significantly reduce assembly compute resources and time. The paper demonstrates that through the use of SMRT Sequencing, many genomes can now be de novo sequenced and assembled at high quality, including the human genome, using an automated pipeline and without the need for multiple sequencing technologies.
The Nature Methods paper, from scientists at the Icahn School of Medicine at Mount Sinai, Cold Spring Harbor Laboratory, and other institutions, reports an assembly of a diploid human genome using a combination of SMRT Sequencing and genome maps. The hybrid genome assembly “represents the most contiguous clone-free genome assembly ever made, and is comparable to, or better than, other human assemblies employing mixtures of fosmid or BAC libraries,” according to the authors. The study also reports the calling of a comprehensive set of structural variants and tandem repeats (TRs) using their de novo assembled genome and phasing of these variants onto maternal and paternal alleles. TRs, known to cause significant repeat expansion disorders such as Fragile X and
Myotonic Dystrophy, have been under-studied in human genome projects due to the inability of short read methods to span long repeats.
“The Mt. Sinai and NBACC studies are significant because high-quality genome assembly has not previously been possible without expensive manual finishing,” said Dr. Jonas Korlach, Chief Scientific Officer of Pacific Biosciences. “Further, both of these research teams were able to completely reconstruct human genomes from scratch using their new long-read de novo assembly methods, with quality levels that exceeded the initial draft produced from the Human Genome Project. These new methods will provide exciting opportunities for the community to generate both personal reference genome assemblies and population-specific reference genome assemblies with PacBio sequencing at a very reasonable cost.”
In BMC Genomics, a team of scientists led by the Human Genome Sequencing Center at Baylor College of Medicine present a thorough analysis of the structural variation found in a diploid human genome. By adding just 10x PacBio sequence read coverage of and using their PBHoney SV detection software, the researchers more than tripled the number of structural variants detected by other technologies, demonstrating long-read data is ideally suited to calling these complex genomic elements. As part of this work, the scientists developed a structural variant integration and evaluation pipeline named Parliament, which is now publicly available for download and through DNAnexus.
“The Baylor study reiterated that structural variants account for the majority of variable bases in individual genomes, and that most of these SVs are missed using short-read sequencing methods alone,” said Dr. Michael Hunkapiller, President and CEO of Pacific Biosciences. “This is significant because structural variants have been implicated in a broad variety of diseases, like ALS, autism, and cancer. Thanks to the efforts of scientists at Baylor, and other institutions, the scientific community will now have the option of adding PacBio reads to their human genome projects to reduce the chance of missing something important.”
He added: “These studies pave the way for future projects, and provide a direct path for use of PacBio sequencing under new NIH funding announcements focused on truly whole human genome sequencing and structural variant analysis.”
Konstantin Berlin and Sergey Koren, et al. “Assembling Large Genomes with Single-Molecule Sequencing and Locality Sensitive Hashing.” Nature Biotechnology doi:10.1038/nbt.3238.
M. Pendleton, R. Sebra, A.W.C. Pang, et al. “Assembly and Diploid Architecture of an Individual Human Genome via Single Molecule Technologies.” Nature Methods doi:10.1038/nmeth.3454.
Adam English and William Salerno, et al. “Assessing structural variation in a personal genome—towards a human reference diploid genome.” BMC Genomics doi:10.1186/s12864-015-1479-3.
About Pacific Biosciences
Pacific Biosciences of California, Inc. (NASDAQ:PACB) offers the PacBio® RS II Sequencing System to help scientists resolve genetically complex problems. Based on its novel Single Molecule, Real-Time (SMRT®) technology, Pacific Biosciences’ products enable: de novo genome assembly to finish genomes in order to more fully identify, annotate and decipher genomic structures; full-length transcript analysis to improve annotations in reference genomes, characterize alternatively spliced isoforms in important gene families, and find novel genes; targeted sequencing to more comprehensively characterize genetic variations; and DNA base modification identification to help characterize epigenetic regulation and DNA damage. Pacific Biosciences’ technology provides the industry’s highest consensus accuracy over
the longest read lengths in combination with the ability to detect real-time kinetic information. The PacBio RS II System, including consumables and software, provides a simple, fast, end-to-end workflow for SMRT Sequencing. More information is available at www.pacb.com.
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Source: Pacific Biosciences of California, Inc.
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