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Thursday, August 19, 2021

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, June 1, 2021

Whole genome sequencing and epigenome characterization of cancer cells using the PacBio platform.

The comprehensive characterization of cancer genomes and epigenomes for understanding drug resistance remains an important challenge in the field of oncology. For example, PC-9, a non-small cell lung cancer (NSCL) cell line, contains a deletion mutation in exon 19 (DelE746A750) of EGRF that renders it sensitive to erlotinib, an EGFR inhibitor. However, sustained treatment of these cells with erlotinib leads to drug-tolerant cell populations that grow in the presence of erlotinib. However, the resistant cells can be resensitized to erlotinib upon treatment with methyltransferase inhibitors, suggesting a role of epigenetic modification in development of drug resistance. We have characterized for…

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Tuesday, June 1, 2021

Highly contiguous de novo human genome assembly and long-range haplotype phasing using SMRT Sequencing

The long reads, random error, and unbiased sampling of SMRT Sequencing enables high quality, de novo assembly of the human genome. PacBio long reads are capable of resolving genomic variations at all size scales, including SNPs, insertions, deletions, inversions, translocations, and repeat expansions, all of which are important in understanding the genetic basis for human disease and difficult to access via other technologies. In demonstration of this, we report a new high-quality, diploid aware de novo assembly of Craig Venter’s well-studied genome.

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Tuesday, June 1, 2021

Detection of structural variants using third generation sequencing

Structural Variants (SVs), which include deletions, insertions, duplications, inversions and chromosomal rearrangements, have been shown to effect organism phenotypes, including changing gene expression, increasing disease risk, and playing an important role in cancer development. Still it remains challenging to detect all types of SVs from high throughput sequencing data and it is even harder to detect more complex SVs such as a duplication nested within an inversion. To overcome these challenges we developed algorithms for SV analysis using longer third generation sequencing reads. The increased read lengths allow us to span more complex SVs and accurately assess SVs in repetitive…

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Tuesday, June 1, 2021

Comprehensive genome and transcriptome structural analysis of a breast cancer cell line using PacBio long read sequencing

Genomic instability is one of the hallmarks of cancer, leading to widespread copy number variations, chromosomal fusions, and other structural variations. The breast cancer cell line SK-BR-3 is an important model for HER2+ breast cancers, which are among the most aggressive forms of the disease and affect one in five cases. Through short read sequencing, copy number arrays, and other technologies, the genome of SK-BR-3 is known to be highly rearranged with many copy number variations, including an approximately twenty-fold amplification of the HER2 oncogene. However, these technologies cannot precisely characterize the nature and context of the identified genomic events…

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Tuesday, June 1, 2021

Highly contiguous de novo human genome assembly and long-range haplotype phasing using SMRT Sequencing

The long reads, random error, and unbiased sampling of SMRT Sequencing enables high quality, de novo assembly of the human genome. PacBio long reads are capable of resolving genomic variations at all size scales, including SNPs, insertions, deletions, inversions, translocations, and repeat expansions, all of which are both important in understanding the genetic basis for human disease, and difficult to access via other technologies. In demonstration of this, we report a new high-quality, diploid-aware de novo assembly of Craig Venter’s well-studied genome.

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Tuesday, June 1, 2021

Joint calling and PacBio SMRT Sequencing for indel and structural variant detection in populations

Fast and effective variant calling algorithms have been crucial to the successful application of DNA sequencing in human genetics. In particular, joint calling – in which reads from multiple individuals are pooled to increase power for shared variants – is an important tool for population surveys of variation. Joint calling was applied by the 1000 Genomes Project to identify variants across many individuals each sequenced to low coverage (about 5-fold). This approach successfully found common small variants, but broadly missed structural variants and large indels for which short-read sequencing has limited sensitivity. To support use of large variants in rare…

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Tuesday, June 1, 2021

Structural variant detection with long read sequencing reveals driver and passenger mutations in a melanoma cell line

Past large scale cancer genome sequencing efforts, including The Cancer Genome Atlas and the International Cancer Genome Consortium, have utilized short-read sequencing, which is well-suited for detecting single nucleotide variants (SNVs) but far less reliable for detecting variants larger than 20 base pairs, including insertions, deletions, duplications, inversions and translocations. Recent same-sample comparisons of short- and long-read human reference genome data have revealed that short-read resequencing typically uncovers only ~4,000 structural variants (SVs, =50 bp) per genome and is biased towards deletions, whereas sequencing with PacBio long-reads consistently finds ~20,000 SVs, evenly balanced between insertions and deletions. This discovery has…

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Tuesday, June 1, 2021

Structural variant detection in crops using low-fold coverage long-read sequencing

Genomics studies have shown that the insertions, deletions, duplications, translocations, inversions, and tandem repeat expansions in the structural variant (SV) size range (>50 bp) contribute to the evolution of traits and often have significant associations with agronomically important phenotypes. However, most SVs are too small to detect with array comparative genomic hybridization and too large to reliably discover with short-read DNA sequencing. While de novo assembly is the most comprehensive way to identify variants in a genome, recent studies in human genomes show that PacBio SMRT Sequencing sensitively detects structural variants at low coverage. Here we present SV characterization in…

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Friday, February 5, 2021

AGBT Conference: Personalized phased diploid genomes of the EN-TEx samples

At AGBT 2017, Mike Schatz from Johns Hopkins University and Cold Spring Harbor Laboratory presented data from sequencing, assembling, and analyzing personalized, phased diploid genomes with either Illumina, 10x Genomics, and PacBio SMRT Sequencing. Compared to the short-read-based methods, PacBio data assembled in large, complete contigs and contained the broadest range of structural variants with the best resolution. Plus: unexpected translocation findings with SMRT Sequencing, validated in follow-up studies.

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Friday, February 5, 2021

Tutorial: Structural variant calling [SMRT Link v6.0.0]

This tutorial provides an overview of the Structural Variant Calling application in SMRT Link and a live demo of how to launch an analysis in SMRT Link and interpret the results. This application identifies large (default: = 20 bp) insertions, deletions, inversions and translocations in a sample relative to a reference from.This tutorial covers features of SMRT Link v6.0.0.

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Friday, February 5, 2021

PAG Conference: Dawn of the crop pangenome era

To make improvements to crops like corn, soybeans, and canola, scientists at Corteva are building a compendium of crop genomics resources to provide actionable sequence info for genetic discovery, gene-editing, and seed product development. Hear how Kevin Fengler, Comparative Genomics Lead of Data Science and Bioinformatics at Corteva, is using PacBio sequences to build visualization tools and genome assembly pipelines as a contribution to this effort.

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Friday, February 5, 2021

ASHG PacBio Workshop: PacBio product updates and roadmap – announcing the release of new chemistry and software

In this ASHG workshop presentation , Jonas Korlach, CSO of PacBio, walked attendees through recent product updates and the coming technology roadmap. The Sequel System 6.0 release offered major improvements to accuracy, throughput, structural variant calling, and large-insert libraries, he said, showing examples of 35 kb libraries. Looking ahead, Korlach said that the V2 express library preparation product should be available early in 2019, with the new 8M SMRT Cell being introduced sometime later.

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Friday, February 5, 2021

Webinar: Amplicon sequencing with confidence – High-fidelity, long-read PacBio sequencing solutions

In this webinar, Lori Aro and Cheryl Heiner of PacBio describe how high-throughput amplicon sequencing using Single Molecule, Real-Time (SMRT) Sequencing and the Sequel System allows for the easy and cost-effective generation of high-fidelity, long reads from amplicons ranging in size from several hundred base pairs to 20 kb. Topics covered include the latest advances in SMRT Sequencing performance for detection of all variant types even in difficult to sequence regions of the genome, multiplexing options to increase throughput and improve efficiency, and examples of amplicon sequencing of clinically relevant targets.

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