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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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Monday, May 17, 2021

The Utility of HiFi Long-Read WGS in Solving Patients with Rare Diseases

In this talk, Dr. Matsumoto describes his research of a family with syndromic intellectual disability. Trio-base exome analysis could not find any culprit mutation. Therefore, he and his team applied trio-based HiFi long-read WGS using two flowcells for a patient and one flowcell each for her father and mother. Through systematic variant filtering, they could find a 12-kb copy neutral inversion disrupting a causative gene. In addition, they could confirm that the de novo inversion occurred on the paternal chromosome through the haplotype phasing. These data demonstrate the utility of HiFi long-read WGS in solving patients with rare diseases.

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Monday, May 17, 2021

The Present and Future of HiFi Whole-Genome Sequencing for Rare Disease

In this talk, Dr. Wenger describes how whole-genome sequencing (WGS) with accurate, long HiFi reads identify all the variations found with short reads plus small variants in difficult-to-map regions and structural variants across the genome. He further explains how HiFi reads also support direct phasing of variants into haplotypes. Researchers worldwide apply HiFi reads to explain rare disease cases unsolved by other technologies. Improvements in workflow, reliability, cost and throughput support the routine application of HiFi reads in large studies today and open a future of HiFi genomes as a standard tool for rare disease researchers.

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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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Friday, April 23, 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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