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Tuesday, June 1, 2021

Comprehensive structural and copy-number variant detection with long reads

To comprehensively detect large variants in human genomes, we have extended pbsv – a structural variant caller for long reads – to call copy-number variants (CNVs) from read-clipping and read-depth signatures. In human germline benchmark samples, we detect more than 300 CNVs spanning around 10 Mb, and we call hundreds of additional events in re-arranged cancer samples. Long-read sequencing of diverse humans has revealed more than 20,000 insertion, deletion, and inversion structural variants spanning more than 12 Mb in a typical human genome. Most of these variants are too large to detect with short reads and too small for array…

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Tuesday, June 1, 2021

Detection and phasing of small variants in Genome in a Bottle samples with highly accurate long reads

Introduction: Long-read PacBio SMRT Sequencing has been applied successfully to assemble genomes and detect structural variants. However, due to high raw read error rates of 10-15%, it has remained difficult to call small variants from long reads. Recent improvements in library preparation, sequencing chemistry, and instrument yield have increased length, accuracy, and throughput of PacBio Circular Consensus (CCS) reads, resulting in 10-20 kb “HiFi” reads with mean read quality above 99%. Materials and Methods: We sequenced 11 kb size-selected libraries from the Genome in a Bottle (GIAB) human reference samples HG001, HG002, and HG005 to approximately 30-fold coverage on the…

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Tuesday, June 1, 2021

Beyond Contiguity: Evaluating the accuracy of de novo genome assemblies

HiFi reads (>99% accurate, 15-20 kb) from the PacBio Sequel II System consistently provide complete and contiguous genome assemblies. In addition to completeness and contiguity, accuracy is of critical importance, as assembly errors complicate downstream analysis, particularly by disrupting gene frames. Metrics used to assess assembly accuracy include: 1) in-frame gene count, 2) kmer consistency, and 3) concordance to a benchmark, where discordances are interpreted as assembly errors. Genome in a Bottle (GIAB) provides a benchmark for the human genome with estimated accuracy of 99.9999% (Q60). Concordance for human HiFi assemblies exceeds Q50, which provides excellent genomes for downstream analysis,…

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Tuesday, June 1, 2021

Copy-number variant detection with PacBio long reads

Long-read sequencing of diverse humans has revealed more than 20,000 insertion, deletion, and inversion structural variants spanning more than 12 Mb in a healthy human genome. Most of these variants are too large to detect with short reads and too small for array comparative genome hybridization (aCGH). While the standard approaches to calling structural variants with long reads thrive in the 50 bp to 10 kb size range, they tend to miss exactly the large (>50 kb) copy-number variants that are called more readily with aCGH. Standard algorithms rely on reference-based mapping of reads that fully span a variant or…

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Tuesday, June 1, 2021

Metagenomic analysis of type II diabetes gut microbiota using PacBio HiFi reads reveals taxonomic and functional differences

In the past decade, the human microbiome has been increasingly shown to play a major role in health. For example, imbalances in gut microbiota appear to be associated with Type II diabetes mellitus (T2DM) and cardiovascular disease. Coronary artery disease (CAD) is a major determinant of the long-term prognosis among T2DM patients, with a 2- to 4-fold increased mortality risk when present. However, the exact microbial strains or functions implicated in disease need further investigation. From a large study with 523 participants (185 healthy controls, 186 T2DM patients without CAD, and 106 T2DM patients with CAD), 3 samples from each…

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Tuesday, June 1, 2021

A workflow for the comprehensive detection and prioritization of variants in human genomes with PacBio HiFi reads

PacBio HiFi reads (minimum 99% accuracy, 15-25 kb read length) have emerged as a powerful data type for comprehensive variant detection in human genomes. The HiFi read length extends confident mapping and variant calling to repetitive regions of the genome that are not accessible with short reads. Read length also improves detection of structural variants (SVs), with recall exceeding that of short reads by over 30%. High read quality allows for accurate single nucleotide variant and small indel detection, with precision and recall matching that of short reads. While many tools have been developed to take advantage of these qualities…

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Tuesday, June 1, 2021

Comprehensive variant detection in a human genome with highly accurate long reads

Introduction: Long-read sequencing has revealed more than 20,000 structural variants spanning over 12 Mb in a healthy human genome. Short-read sequencing fails to detect most structural variants but has remained the more effective approach for small variants, due to 10-15% error rates in long reads, and copy-number variants (CNVs), due to lack of effective long-read variant callers. The development of PacBio highly accurate long reads (HiFi reads) with read lengths of 10-25 kb and quality >99% presents the opportunity to capture all classes of variation with one approach.Methods: We sequence the Genome in a Bottle benchmark sample HG002 and an…

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Friday, February 5, 2021

User Group Meeting: Unbiased characterization of metagenome composition and function using HiFi sequencing on the PacBio Sequel II System

In this PacBio User Group Meeting presentation, PacBio scientist Meredith Ashby shared several examples of analysis — from full-length 16S sequencing to shotgun sequencing — showing how SMRT Sequencing enables accurate representation for metagenomics and microbiome characterization, in some cases even without fully assembling genomes. New updates will provide users with a dedicated microbial assembly pipeline, optimized for all classes of bacteria, as well as increased multiplexing on the Sequel II System, now with 48 validated barcoded adapters. That throughput could reduce the cost of microbial analysis substantially.

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Friday, February 5, 2021

Webinar: Variant calling and de novo genome assembly with PacBio HiFi reads

In this webinar, Sarah Kingan, Staff Scientist, PacBio, presents recent work on de novo genome assembly using PacBio HiFi reads. She highlights the benefits of HiFi data for base level accuracy, haplotype phasing, and ease of computation. And in samples ranging from human to plants, she benchmarks various tools for HiFi assembly and phasing, including the newly extended FALCON-Unzip assembler. Subsequently, Andrew Carroll, Genomics Product Lead, GoogleAI, explores how the GoogleAI team retrained DeepVariant, a highly accurate SNP and Indel caller, for PacBio HiFi data. The resulting DeepVariant models achieve comparable accuracies to short-read methods with the additional benefit of…

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Friday, February 5, 2021

Webinar: Unbiased, efficient characterization of metagenome functions with PacBio HiFi sequencing

Understanding interactions among plants and the complex communities of organisms living on, in and around them requires more than one experimental approach. A new method for de novo metagenome assembly, PacBio HiFi sequencing, has unique strengths for determining the functional capacity of metagenomes. With HiFi sequencing, the accuracy and median read length of unassembled data outperforms the quality metrics for many existing assemblies generated with other technologies, enabling cost-competitive recovery of full-length genes and operons even from rare species. When paired with the ability to close the genomes of even challenging isolates like Xanthomonas, the PacBio Sequel II System is…

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Friday, February 5, 2021

Webinar: A HiFi View – Sequencing the gut microbiome with highly accurate long reads

In this webinar, Dr. Ashby gives attendees a brief update on PacBio’s metagenomics solutions on the Sequel II System. Then, Dr. Ma, University of Maryland School of Medicine, discusses her work using long read sequencing to identify high-resolution microbial biomarkers associated with leaky gut syndrome in premature infants. Finally, Dr. Weinstock, The Jackson Laboratory, talks about the potential of highly accurate long reads to enable strain-level resolution of the human gut microbiome by resolving intraspecies variation in multiple copies of the 16S gene.

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Friday, February 5, 2021

Webinar: Sequencing 101 – How long-read sequencing improves access to genetic information

In this webinar, Kristin Mars, Sequencing Specialist, PacBio, presents an introduction to PacBio’s technology and its applications followed by a panel discussion among sequencing experts. The panel discussion addresses such things as what long reads are and how are they useful, what differentiates PacBio long-read sequencing from other technologies, and the applications PacBio offers and how they can benefit scientific research.

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Friday, February 5, 2021

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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