Discover the benefits of HiFi reads and learn how highly accurate long-read sequencing provides a single technology solution across a range of applications.
PacBio HiFi reads provide both long read lengths (up to 25 kb) and high accuracy (>99.9%) to quickly and affordably generate contiguous, complete, and correct de novo genome assemblies of even the most complex genomes.
This landmark study by members of the Telomere-to-Telomer Consortium is the first fully complete assembly to be produced 20 years after the initial drafts of the human genome.
In this video Shawn Levy, Discovery Life Sciences’ Chief Scientific Officer, along with Cheryl Heiner, PacBio Principal Scientist, discuss the advantages of HudsonAlpha Discovery’s specialized sequencing services for PacBio HiFi…
In this talk, speakers provide an understanding HiFi sequencing methods for resolving viral diversity in complex systems, examples of how HiFi sequencing can phase entire viral genes or genomes, revealing…
In this talk, speakers provide an overview of PacBio-recommended tools for metagenome sequencing analysis, where to download example test data, the typical performance for HiFi metagenome sequencing of fecal samples,…
In this SMRT Science Journal Club talk, Anoushka Joglekar from Weill Cornell Medicine discusses how she and her colleagues are developing tools to produce an isoform view of the brain…
In this SMRT Science Journal Club talk, Phillip Tai from the University of Massachusetts Medical School discusses his investigation in the design compatibility of CRISPR components in AAV vectors.
Spinocerebellar ataxia type 10 (SCA10) is a rare autosomal-dominant disorder caused by an expanded intronic pentanucleotide repeat in the ATXN10 gene. This repeat expansion when fully penetrant can be typically…
Many neurological diseases result from expansion of unstable variable nucleotide tandem repeats (VNTRs) that influence gene transcription of neighboring genes. In this talk, Dr. Henne Holstege presents research that investigated…
Through Pharmacogenomics (PGx), we can explore how a person’s genome affects their response to drugs to enable the development of safe and effective medications tailored to their genetic makeup. In…
Colorectal cancer (CRC) represents one of the most prevalent and lethal malignant neoplasms and every individual of age 50 and above should undergo regular CRC screening. Currently, the most effective procedure to detect adenomas, the precursors to CRC, is colonoscopy, which reduces CRC incidence by 80%. However, it is an invasive approach that is unpleasant for the patient, expensive, and poses some risk of complications such as colon perforation. A non-invasive screening approach with detection rates comparable to those of colonoscopy has not yet been established. The current study applies Pacific Biosciences third generation, single molecule sequencing to the inspection of CRC-driving mutations. Our approach combines the screening power and the extremely high accuracy of circular consensus (CCS) third generation sequencing with the non-invasiveness of using stool DNA to detect CRC-associated mutations present at extremely low frequencies and establishes a foundation for a non-invasive, highly sensitive assay to screen the population for CRC and early stage adenomas. We performed a series of experiments using a pool of fifteen amplicons covering the genes most frequently mutated in CRC (APC, Beta Catenin, KRAS, BRAF, and TP53), ensuring a theoretical screening coverage of over 97% for both CRC and adenomas. The assay was able to detect mutations in DNA isolated from stool samples from patients diagnosed with CRC at frequencies below 0.5 % with no false positives. The mutations were then confirmed by sequencing DNA isolated from the excised tumor samples. Our assay should be sensitive enough to allow the early identification of adenomatous polyps using stool DNA as analyte. In conclusion, we have developed an assay to detect mutations in the genes associated with CRC and adenomas using Pacific Biosciences RS Single Molecule, Real Time Circular Consensus Sequencing (SMRT-CCS). With no systematic bias and a much higher raw base-calling quality (CCS) compared to other sequencing methods, the assay was able to detect mutations in stool DNA at frequencies below 0.5 % with no false positives. This level of sensitivity should be sufficient to allow the detection of most adenomatous polyps using stool DNA as analyte, a feature that would make our approach the first non-invasive assay with a sensitivity comparable to that of colonoscopy and a strong candidate for the non-invasive preventive CRC screening of the general population.
High-throughput sequencing of the complete 16S rRNA gene has become a valuable tool for characterizing microbial communities. However, the short reads produced by second-generation sequencing cannot provide taxonomic classification below the genus level. In this study, we demonstrate the capability of PacBio’s Single Molecule, Real-Time (SMRT) Sequencing to generate community profiles using mock microbial community samples from BEI Resources. We also evaluate multiplexing capabilities using PacBio barcodes on pooled samples comprising heterogeneous 16S amplicon populations representing soil, fecal, and mock communities.
Numerous whole genome sequencing projects already achieved or ongoing have highlighted the fact that obtaining a high quality genome sequence is necessary to address comparative genomics questions such as structural variations among genotypes and gain or loss of specific function. Despite the spectacular progress that has been done regarding sequencing technologies, accurate and reliable data are still challenging, at the whole genome scale but also when targeting specific genomic regions. These issues are even more noticeable for complex plant genomes. Most plant genomes are known to be particularly challenging due to their size, high density of repetitive elements and various levels of ploidy. To overcome these issues, we have developed a strategy in order to reduce the genome complexity by using the large insert BAC libraries combined with next generation sequencing technologies. We have compared two different technologies (Roche-454 and Pacific Biosciences PacBio RS II) to sequence pools of BAC clones in order to obtain the best quality sequence. We targeted nine BAC clones from different species (maize, wheat, strawberry, barley, sugarcane and sunflower) known to be complex in terms of sequence assembly. We sequenced the pools of the nine BAC clones with both technologies. We have compared results of assembly and highlighted differences due to the sequencing technologies used. We demonstrated that the long reads obtained with the PacBio RS II technology enables to obtain a better and more reliable assembly notably by preventing errors due to duplicated or repetitive sequences in the same region.
Scientists who require confident resolution of heterogeneous populations across complex regions have been unable to transition to short-read sequencing methods. They continue to depend on Sanger Sequencing despite its cost and time inefficiencies. Here we present a new redesigned algorithm that allows the generation of circular consensus sequences (CCS) from individual SMRT Sequencing reads. With this new algorithm, dubbed CCS2, it is possible to reach arbitrarily high quality across longer insert lengths at a lower cost and higher throughput than Sanger Sequencing. We apply this new algorithm, dubbed CCS2, to the characterization of the HIV-1 K103N drug-resistance associated mutation, which is both important clinically, and represents a challenge due to regional sequence context. A mutation was introduced into the 3rd position of amino acid position 103 (A>C substitution) of the RT gene on a pNL4-3 backbone by site-directed mutagenesis. Regions spanning ~1,300 bp were PCR amplified from both the non-mutated and mutant (K103N) plasmids, and were sequenced individually and as a 50:50 mixture. Sequencing data were analyzed using the new CCS2 algorithm, which uses a fully-generative probabilistic model of our SMRT Sequencing process to polish consensus sequences to arbitrarily high accuracy. This result, previously demonstrated for multi-molecule consensus sequences with the Quiver algorithm, is made possible by incorporating per-Zero Mode Waveguide (ZMW) characteristics, thus accounting for the intrinsic changes in the sequencing process that are unique to each ZMW. With CCS2, we are able to achieve a per-read empirical quality of QV30 with 19X coverage. This yields ~5000 1.3 kb consensus sequences with a collective empirical quality of ~QV40. Additionally, we demonstrate a 0% miscall rate in both unmixed samples, and estimate a 48:52% frequency for the K103N mutation in the mixed sample, consistent with data produced by orthogonal platforms.
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