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Wednesday, June 23, 2021

Application Brief: Variant detection using whole genome sequencing with HiFi reads – Best Practices

With highly accurate long reads (HiFi reads) from the Sequel II or IIe Systems you can comprehensively detect variants in 100s to 1000s of genomes in a year. HiFi reads provide high precision and recall for single nucleotide variants (SNVs), indels, structural variants (SVs), and copy number variants (CNVs), including in difficult-to-map repetitive regions.

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Wednesday, June 23, 2021

Application Brochure: Scalable human whole genome HiFi sequencing for rare and inherited disease research

PacBio highly accurate long reads – HiFi reads – offer a single-platform solution for rare and inherited disease research, elucidating suspected genetic causes of disease in up to ~50% of cases that have not previously been explained using short-read exome or whole genome sequencing. PacBio offers an efficient workflow, developed in collaboration with Children’s Mercy Kansas City, which provides a scalable solution for sequencing 100s to 1000s of whole human genomes per year on the Sequel II and Sequel IIe Systems.

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Tuesday, June 1, 2021

Improving the reference with a diversity panel of sequence-resolved structural variation

Although the accuracy of the human reference genome is critical for basic and clinical research, structural variants (SVs) have been difficult to assess because data capable of resolving them have been limited. To address potential bias, we sequenced a diversity panel of nine human genomes to high depth using long-read, single-molecule, real-time sequencing data. Systematically identifying and merging SVs =50 bp in length for these nine and one public genome yielded 83,909 sequence-resolved insertions, deletions, and inversions. Among these, 2,839 (2.0 Mbp) are shared among all discovery genomes with an additional 13,349 (6.9 Mbp) present in the majority of humans,…

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Monday, May 24, 2021

Complete and Accurate Human Genomes with HiFi Reads

In this CSHL Biology of Genomes 2021 virtual workshop, Aaron Wenger from PacBio discusses examples of how advances in highly accurate long-read (HiFi) sequencing have enabled exciting developments in human genome research, including sequencing the genomes of 100 individuals with unexplained diseases.

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Monday, May 17, 2021

Genomic Answers for Kids

Short-read genome-wide sequencing for molecular diagnosis has revolutionized pediatric rare disease care in the past decade. However, most families remain without specific knowledge of the cause of their child’s illness. We seek to understand how long-read sequencing (HiFi sequencing) and functional genomics can fill the gaps and identify most causes of genetic disease. Dr. Pastinen describes a health-system-wide initiative to translate the latest research approaches to end the diagnostic “odyssey” affecting rare disease families, observing an expanded range of variation and enhanced interpretation of known variation by integrating HiFi data to unsolved rare disease cases.

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Monday, May 17, 2021

A Bioinformatics Workflow for Comprehensive Detection and Prioritization of Variants with PacBio HiFi Reads

Over the past few years, many tools have been developed to enable comprehensive variant detection from PacBio HiFi reads. This talk describes a flexible, modular workflow for variant detection and prioritization from HiFi whole-genome sequencing data, including open-source tools for quality control, alignment, small variant detection, and phasing, structural variant detection, genotyping of tandem repeats, and de novo assembly. This pipeline is available on GitHub as a Snakemake workflow and has been adapted into a Cromwell WDL workflow by Microsoft Genomics.

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Monday, May 17, 2021

Long Reads to Identify Hidden Structural Variants in Rare Disease

Alexander Hoischen’s research group ‘Genomic Technologies and Immuno-Genomics’ has expertise in the identification of rare disease genes using the latest genomics tools, with a recent particular focus on immune-related disease genes. His group has been the first to identify a disease causing dominant de novo mutation for a Mendelian disorder by exome sequencing, followed by the identification of several disease genes for rare diseases. Following a six-month research stint in 2013 in the laboratories of collaborators, Prof. Eichler and Prof. Shendure (UW, Seattle; USA), Dr. Hoischen established the latest technology for accurate and large-scale targeted re-sequencing (smMIPs) in Nijmegen. Recently,…

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Monday, May 17, 2021

Scalable Workflow for Constructing HiFi Libraries

In this talk, Christine Lambert describes a simple and scalable workflow for generating high-quality HiFi reads appropriate for comprehensive variant detection (SNVs, Indels, SVs) and de novo assembly. Using this workflow, multiple samples can be processed manually (up to 16) with a multichannel pipet and strip tubes. Up to 96 samples can be processed on an automated liquid handler such as the Sciclone Liquid Handler Workstation. She also describes solutions for high-throughput SMRTbell library construction for generating HiFi reads on the Sequel IIe System.

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