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Thursday, October 10, 2019

Review: Long-Read Sequencing Helps Uncover Genetic Basis for Rare Disease

A new review article nicely sums up the utility of long-read sequencing for solving rare diseases that cannot be explained by other methods. The paper, published in the Journal of Human Genetics, comes from authors Satomi Mitsuhashi and Naomichi Matsumoto at Yokohama City University in Japan. The scientists note that long-read sequencing serves as a good complementary approach for cases that are not solved with short-read sequencing alone. “The approximate current diagnostic rate is <50% using [short-read whole exome and genome sequencing], and there remain many rare genetic diseases with unknown cause,” Mitsuhashi and Matsumoto write. “There may be many…

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Monday, June 17, 2019

Broad Institute Scientists Use Sequel II System for Trios, Structural Variant Detection

Kiran Garimella As we geared up for the launch of our new Sequel II System, we had the good fortune of working closely with several expert customers in an early access program. Recently, three of those customers reported on their experience with the new sequencing system in a webinar. In this blog series, we’ll be summarizing each speaker’s presentation, and the full recording is available to view. First up was Kiran Garimella (@KiranGarimella), a senior computational scientist at the Broad Institute who focused on the use of HiFi reads, which are long (>10 kb) and accurate (>99%) sequences produced by…

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Tuesday, June 11, 2019

Genome in a Bottle Consortium Describes Human Genome Structural Variation Benchmark

A preprint released this week from the Genome in a Bottle (GIAB) Consortium describes a benchmark set of structural variants (SVs), differences ≥50 bp, in the genome of a human male named HG002. The GIAB benchmark is the first to allow measuring precision (false positives) and recall (false negatives) of different approaches to detecting structural variants. The GIAB Consortium also developed a tool, Truvari, to support evaluation of variant call sets against the benchmark. Earlier GIAB benchmarks, first released in 2014 and last updated in 2017, have led to enormous improvements in the quality and consistency of calling single-nucleotide and…

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Thursday, May 23, 2019

Review: How Long-Read Sequencing Could Make a Difference in Medical Genetics

A recent review article published in Frontiers in Genetics offers a great look at the landscape of long-read sequencing. Authors Tuomo Mantere, Simone Kersten, and Alexander Hoischen from Radboud University Medical Center in the Netherlands focus on emerging applications in medical genetics for long-read technologies. “With the recently demonstrated success in identifying previously intractable DNA sequences and closing gaps in the human genome assemblies, long-read sequencing (LRS) technologies hold the promise to overcome specific limitations of NGS-based investigations of human diseases,” the scientists write. “LRS has the potential to grow into a technology that is used not only to produce…

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