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Thursday, August 27, 2020

Human Biomedical Research Brochure: The most comprehensive view of the human genome

To understand the genetic factors underlying health and disease and to address hidden heritability, scientists require a more comprehensive view of all the variations in the human genome. Single Molecule, Real-Time (SMRT) Sequencing delivers the read lengths, uniform coverage, and accuracy needed for accessing the complete size spectrum of sequence variant types — from single nucleotides to complex structural variants. PacBio’s long single-molecule reads also provide direct variant phasing information across full-length genes and chromosome haplotype blocks. With SMRT Sequencing, scientists gain new insight into the genetic basis of health and disease.

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Thursday, August 27, 2020

Whitepaper: Structural variation in the human genome

Structural variation accounts for much of the variation among human genomes. Structural variants of all types are known to cause Mendelian disease and contribute to complex disease. Learn how long-read sequencing is enabling detection of the full spectrum of structural variants to advance the study of human disease, evolution and genetic diversity.

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Tuesday, April 21, 2020

SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica).

The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica).As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label…

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Tuesday, April 21, 2020

The tech for the next decade: promises and challenges in genome biology.

The 19th Annual Advances in Genome Biology and Technology (AGBT) meeting came back to Marco Island, Florida, and was held in the renovated venue from 27 February to 2 March 2019. The meeting showed a variety of new technology, both in wet lab and in bioinformatics. This year’s themes included single-cell technology and applications, spatially resolved gene expression measurements, new sequencing platforms, genome assembly and variation, and long and linked reads.

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Monday, March 30, 2020

AGBT Presentation: The Sequel II System – The next evolution of SMRT Sequencing

In this AGBT presentation, Marty Badgett shares a look at the latest results from circular consensus sequencing (CCS) mode for highly accurate reads and data from our soon-to-be-released Sequel II System. As he demonstrates, CCS reads cover the same molecule many times, delivering high consensus accuracy despite noisy raw reads; on average, reaching 10 passes achieves Q30 accuracy. Badgett offers several examples where this is useful, such as pharmacogenomic gene analysis and resolving metagenomic communities. He also provides an update on the Iso-Seq method, which can now segregate transcripts into haplotype-specific alleles using a new tool called Iso-Phase.

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Monday, March 30, 2020

AGBT Presentation: HiFi long reads for comprehensive genomic analysis

In this AGBT presentation, Mike Hunkapiller shares insights on using highly accurate long (HiFi) reads generated in circular consensus sequencing (CCS) mode for comprehensive genomic analysis and provides examples such as the sequencing of a Genome in a Bottle reference sample, which concluded with Q48 accuracy, 18 Mb contigs, and clearly phased haplotypes.

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Monday, March 30, 2020

AGBT Presentation: Single cell isoform sequencing (scIso-Seq) identifies novel full-length mRNAs and cell type-specific expression

In this AGBT presentation from AGBT 2019, Jason Underwood, shares information about single-cell isoform sequencing (scIso-Seq), focusing on a collaborative project with the labs of Evan Eichler and Alex Pollen. For this effort, scientists used Drop-seq sample prep and then loaded cDNA products onto the Sequel System. Results from a barnyard experiment using mouse and human cells as well as from cerebral organoids demonstrated that this approach could deliver cell type-specific gene expression data. Underwood also presents data from the Sequel II System comparing chimp and human organoids, resulting in information about 14,000 unique genes with important insights for post-transcriptional…

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Monday, March 30, 2020

AGBT Presentation: Studying CRISPR guide RNA specificity by amplification-free long-read sequencing

At AGBT 2020, Adam Ameur from Uppsala University discussed the use of long-read PacBio sequencing to detect off-target results from CRISPR/Cas9 gene editing studies. His team uses HiFi reads from the Sequel II System to perform whole genome sequencing and figure out exactly where guide RNAs bind. In one example using a human embryonic kidney cell line, they found 55 off-target sites for three guide RNAs. Ameur’s group has already generated preliminary data on results from editing living cells.

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Monday, March 30, 2020

AGBT Presentation: Generating high quality human reference assemblies with PacBio sequencing

Tina Graves-Lindsay from the McDonnell Genome Institute reports at AGBT 2020 on how her team is using PacBio sequencing to produce reference-grade human genome assemblies. With highly accurate HiFi reads, no error correction step is needed during the sequencing and analysis process, and they can produce reference-grade assemblies with half the sequence coverage needed before. They are now generating diploid assemblies and will be contributing to the human pangenome reference project.

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Monday, March 30, 2020

AGBT Presentation: Feed the World – Developing genomic resources for insects as food

In a push to develop insect-based food sources for people, Brenda Oppert from the USDA has been sequencing bug genomes with PacBio technology. Long reads are essential because of the highly repetitive sequences and large genomes. On the Sequel II System, a single SMRT Cell is sufficient to generate 350-fold coverage and produce a high-quality assembly for some of the insects she’s studying.

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Monday, March 30, 2020

AGBT 2015 Highlights: Customer interviews day 1

PacBio customers discuss their applications of PacBio SMRT Sequencing and long reads, including Lemuel Racacho (Children’s Hospital of Eastern Ontario Research Institute), Matthew Blow (JGI), Yuta Suzuki (U. of Tokyo), Daniel Geraghty (Fred Hutchinson Cancer Center), and Mike Schatz (CSHL)

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Monday, March 30, 2020

Customer Experience: At CSHL, new achievements with long-read sequencing

Michael Schatz from Cold Spring Harbor Laboratory talks about using SMRT Sequencing to generate the world’s best crop genome assembly, discovering thousands of gene elements that had never been seen before. He also reports on how long reads made it possible to interrogate a highly complex breast cancer cell line that was too challenging to sequence with previous platforms.

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