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Friday, February 12, 2021

LeafGo: A Workflow That Enables High-Quality Seven-Day Plant Genome Assembly 

A team of scientists from KAUST used a new rapid de novo assembly workflow to create genomes of the Eucalyptus species E. camaldulensis What does the ideal genome assembly look like? High-quality, free of errors, with no gaps, and all haplotypes resolved.  It’s a big ask, especially with challenging genomes like plants that are rich in repetitive content with high levels of heterozygosity and complex polyploidy. Moreover, such assemblies often require a combination of technologies, such as sequencing plus optical mapping.  But a team of scientists at the King Abdullah University of Science and Technology (KAUST) Core Labs (@kaust_corelabs), proved…

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Thursday, January 28, 2021

New Macaque Genome Provides a Big Boost for Biomedical Research

A high resolution reference genome for the rhesus macaque could help us better understand human disease. They may not be as well known as our chimpanzee or gorilla cousins, but macaques have played many key roles in scientific progress over the last half century. From launching into orbit during the early days of space travel to revealing the genetics of neurodevelopmental disorders and infectious diseases today, the rhesus macaque remains a key research primate around the world.   A new, comprehensively annotated reference genome unveiled last month boosts the potential of the most widely used non-human primate in biomedical research even…

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Thursday, January 21, 2021

PacBio-Powered Analysis Indicates Methylation Makes TB Pathogen So Wily

Scientists have long struggled to explain the success of Mycobacterium tuberculosis in the face of effective therapeutics. Tuberculosis (TB) kills more than 1 million people annually, and has a remarkable ability to develop resistance to drugs despite its stable genome. But now, a new study from researchers at San Diego State University and other institutions strongly suggests that methylation rather than genome sequence gives M. tuberculosis its broad phenotypic range. Lead author Samuel Modlin (@sam_modlin), senior author Faramarz Valafar (@FaramarzValafar), and collaborators report using SMRT Sequencing technology to characterize the DNA adenine methylomes of 93 clinical TB isolates. They chose samples representing…

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Friday, January 15, 2021

PacBio and Invitae Team Up to Develop Ultra-High-Throughput Clinical Whole Genome Sequencing Platform

The power of PacBio HiFi reads has enabled transformative research into human disease. A new collaboration with Invitae, a leader in medical genetics, is intended to help harness the technology for use in mainstream medicine.  The ability of HiFi reads to detect genetic variants, even in hard-to-sequence regions of the genome, has already shown clinical utility. In a recent research collaboration with Invitae, announced in October 2020, the comprehensive, highly accurate reads were used to explore clinically relevant molecular targets for use in the development of advanced diagnostic testing for epilepsy.  We are thrilled to announce a new collaboration with…

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Thursday, December 31, 2020

The Most Wonderful Webinars of the Year

The year the world went virtual is virtually over, so what better time to reflect on all the great online offerings featuring SMRT Sequencing this year. While we would have rather gathered in exotic locales to see you in person and share our science, 2020 did provide some amazing opportunities to go global and broadcast worldwide.  Here are some of the highlights:   Sequencing 101: How Long-Read Sequencing Improves Access to Genetic Information What better place to start than with an introduction to our technology, followed by a panel of sequencing experts — Melissa Laird-Smith (@SmithLab_UofL), Michael Hartigan, and Olga…

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Wednesday, December 16, 2020

With Highly Accurate Variant Calling and Phasing, SMRT Sequencing Advances PGx Studies of SLC6A4

Scientists at Stanford University and the Icahn School of Medicine at Mount Sinai have made impressive strides in resolving variants in the SLC6A4 promoter associated with susceptibility to psychiatric disorders and response to antidepressants. This progress was made possible with highly accurate, long-read sequencing, known as HiFi sequencing. Published in the journal Genes, the paper comes from lead author Mariana Botton, senior author Stuart Scott, and collaborators. It describes a SMRT Sequencing-based approach to analyzing amplicons of the SLC6A4 promoter region, which is noted for “a variable number of homologous 20–24 bp repeats,” the authors write, as well as long, extra-long,…

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Monday, December 14, 2020

SMRT Sequencing Offers a Universal Approach for Thalassemia Carrier Testing

Scientists in China have used SMRT Sequencing to demonstrate the value of highly accurate long reads for identifying, linking, and phasing variants associated with a group of blood disorders known collectively as thalassemia. Ultimately, they predict in the Journal of Molecular Diagnostics, long-read sequencing could support a new carrier screening approach for prospective parents interested in knowing their risk of passing these diseases on to their children. “Long molecule sequencing: a new approach for identification of clinically significant DNA variants in alpha and beta thalassemia carriers” comes from lead authors Liangpu Xu, Aiping Mao, and Hui Liu and collaborators at…

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Wednesday, November 25, 2020

Better Apple Pies: HiFi Reads are a Perfect Recipe for High-Quality Apple Genome and Pangenome Assemblies 

Zhangjun Fei inspects a Mutsu apple at Indian Creek Farm in Ithaca, NY. Image credit: Boyce Thompson Institute Scientists at the Boyce Thompson Institute, Cornell University and the USDA Agricultural Research Service have reported significant progress in understanding the genomic features of domestic and wild apples. They used HiFi reads, highly accurate long reads, generated by the Sequel II System to build phased, diploid genome assemblies, as well as apple pangenomes to represent more of the remarkable genetic diversity in this lineage and better characterize its historic domestication.  The paper, published in Nature Genetics, comes from lead authors Xuepeng Sun (@XuepengBio), Chen Jiao, and Heidi Schwaninger; senior author Zhangjun Fei (@fei_lab), and collaborators.  We asked Fei about the highlights of…

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Tuesday, November 17, 2020

Scientists Pinpoint Pathogenic Inversion in Intellectual Disability Case Using HiFi Sequencing

Scientists at Yokohama City University Graduate School of Medicine and Osaka Women’s and Children’s Hospital have discovered a novel pathogenic variant associated with intellectual disability. They made the discovery using HiFi sequencing after previous short-read investigations failed to produce an answer. In the journal Genomics, the team reports the case of 12-year-old monozygotic twin girls who exhibited developmental delays, severely drooping eyelids, and seizures since the age of 5 months. Clinical symptoms matched Dravet syndrome, but no molecular evidence was available to confirm that diagnosis. Their case had previously been analyzed with short-read exome sequencing, but no pathogenic variants were…

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Tuesday, November 10, 2020

Secrets to Longevity Explored in de novo Genome of 115-Year-Old Woman

Hendrikje van Andel-Schipper, at age 108 A new publication from scientists in The Netherlands and Belgium offers tantalizing insights that may shed light on age-related neurodegenerative disorders. The team used SMRT Sequencing to produce a de novo diploid assembly of the genome of a Dutch woman named Hendrikje van Andel-Schipper, who died at the age of 115 with no signs of cognitive decline, and then performed a detailed analysis of variants detected. The data are publicly available to the scientific community. The paper, released in Translational Psychiatry, comes from lead author Jasper Linthorst and senior author Henne Holstege (@HolstegeHenne) at…

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Thursday, October 29, 2020

Breast Cancer Research Legend Mary-Claire King Identifies New Pathogenic Mutation with HiFi Sequencing

Mary-Claire King It’s Breast Cancer Awareness Month, and we can’t think of a better way to celebrate than to honor the passionate scientist who has perhaps single-handedly done more to advance breast cancer research than anyone else alive: Mary-Claire King, discoverer of the BRCA1 and BRCA2 genes. In recognition of her lifelong contributions, King was just awarded the prestigious William Allen Award, the top prize presented annually by the American Society of Human Genetics to recognize substantial and far-reaching scientific contributions to human genetics, carried out over a sustained period of scientific inquiry and productivity. In a recent publication in…

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Monday, October 26, 2020

Egyptian Genome Added to Growing List of Population-Specific Reference Genomes

We’re excited to report that another team has used PacBio long-read sequencing to produce a population-specific reference genome — this time an Egyptian genome that should prove valuable for boosting precision medicine for people of North African ancestry. Lead author Inken Wohlers, senior authors Hauke Busch (@BuschLab) and Saleh Ibrahim, and their collaborators at the University of Lübeck, Mansoura University, and other institutions report their results in Nature Communications. The need for a population-specific reference was clear: the authors note that “only 2% of individuals included in [genome-wide association studies] are of African ancestry” but “genetic disease risk may differ…

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Thursday, October 22, 2020

PacBio and Invitae Team Up to Develop Whole Genome Sequencing-Based Assays for Pediatric Epilepsy Diagnostics

We’re excited to announce a research collaboration with Invitae focused on the investigation of clinically relevant molecular targets for use in the development of advanced diagnostic testing for epilepsy. To support this collaboration, Invitae is expanding its PacBio sequencing capacity to meet the growing demand for clinical applications dependent on highly accurate genomic information. More than half of epilepsies can be traced to a genetic cause. When a child presents with seizures, genetic testing can help identify more than 100 underlying, often rare conditions. Early genetic testing may be the most cost-effective, direct, and accurate diagnostic tool for children, shortening…

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Wednesday, October 21, 2020

The HiFi Sequencing Advantage for Metagenome Assembly

Assembly and binning of metagenome data are the first steps in many metagenomics analysis pipelines, and with good reason. Metagenome assembled genomes (MAGs) and circularized MAGs (CMAGs) allow recovery of complete genes and operons, thereby improving predictions of metabolic capacities. MAGs also provide information about gene synteny and enable better taxonomic profiling. However, as discussed in a recent review by Chen et. al. draft MAGs with poor completeness or high contamination can lead to incorrect conclusions.  One way to improve assembly completeness and contiguity is to use long-read sequencing. However, not all long reads are the same. Did you know…

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Thursday, October 15, 2020

Pediatric Partnership Powered by PacBio Aims to Solve Difficult Rare Disease Cases

Kids have lots of questions. But even the world’s top scientists don’t have all the answers — especially when it comes to rare genetic disorders afflicting children.  Our HiFi reads, highly accurate long reads, generated by our Sequel II and new Sequel IIe Systems, are helping researchers uncover disease-causing genetic variants that had previously gone undetected by other technology, contributing to increased solve rates for rare diseases. We’re particularly excited to see this technology applied to translational research in children. We will be collaborating with Children’s Mercy Kansas City as part of its Genomic Answers for Kids (GA4K) program, which…

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