If only we could track COVID-19 like we track the weather, with satellites and weather stations placed around the globe monitoring and sounding the alarm about potential storms, floods, droughts and other severe weather events. A global pathogen surveillance network would save countless lives, and lessons learned from the current coronavirus pandemic could help make it possible, PacBio Chief Scientific Officer Jonas Korlach told Mendelspod host Theral Timpson (@theraltweet). Korlach joined Brian Caveney, President and Chief Medical Officer of Labcorp, in a recent podcast to discuss SARS-CoV-2 viral surveillance and the trajectory of COVID research, vaccination and treatment. PacBio has…
Today we’re pleased to announce the launch of a new HiFi Sequencing workflow along with a software update for the Sequel II and Sequel IIe Systems that will increase the number of HiFi reads at or above 99.9% accuracy (QV30) for whole genome sequencing-based applications. Together, these advances will improve the quality of HiFi Sequencing while providing an efficient and scalable workflow for sequencing hundreds to thousands of whole human genomes per year on Sequel Systems. This high-throughput sequencing and analysis workflow release includes a new HiFi library prep protocol offering a three-fold reduction in DNA input, enabling HiFi sequencing with limited sample quantities (neonatal…
By Jonas Korlach, Chief Scientific Officer Grapy dusks over tangerine fields. Potato-patch fog over beds of coral. Mountains, glaciers, forests, deserts, fertile farmland and seas with both Arctic and tropical biomes. One of the most geographically and biologically diverse states, California is home to both the highest (Mount Whitney) and lowest (Death Valley) points in the 48 contiguous states, as well as to some of the world’s most exceptional trees — the tallest (coast redwood), most massive (Giant Sequoia), and oldest (bristlecone pine). At PacBio, we are extremely fortunate to have this biodiversity in our back yard —…
When size matters and you need to be able to detect both single nucleotide changes as well as large repeated sequences, SMRT Sequencing on the Sequel II System is the way to go, concluded rare disease researchers at Centre de Recherche en Myologie at Sorbonne Université/INSERM Stéphanie Tomé (@TomeStephanie) and colleagues used the highly sensitive, comprehensive long-read sequencing to investigate myotonic dystrophy type 1 (DM1), the most complex and variable trinucleotide repeat disorder, caused by an unstable CTG repeat expansion that can reach up to 4,000 triplets in those affected most severely with the disease. Myotonic dystrophy type 1 (DM1)…
Scanning electron micrography of human respiratory syncytial virus (RSV) Vaccine safety is of the utmost importance. Respiratory syncytial virus (RSV) is the most common cause of severe lower respiratory tract illness in infants and young children. Much like the flu, it can also cause severe disease in the elderly or immunocompromised adults, making it an important target for vaccine development. In a recently published study, researchers used PacBio long-read sequencing to evaluate the genetic stability of a live-attenuated RSV vaccine candidate and observed previously unknown adaptation mechanisms that was missed by short-read sequencing. Codon-pair deoptimization involves recoding of open reading…
Sequoia sempervirens is one of the tallest living trees on Earth, often reaching up to 300 ft It’s been a year since we took a little field trip to Stanford to collect samples from the giant California redwood (Sequoia sempervirens) with the goal of assembling its ginormous 27 Gb genome. What would have been considered a herculean effort not that many years ago was accomplished in only a few weeks by a handful of personnel —Emily Hatas (@EmilyHatas), Greg Young (@PacbioGreg), Michelle Vierra (@the_mvierra), and Greg Concepcion (@phototrophic) — in their spare time. As detailed in this blog post, the…
Sunday is Rare Disease Day – a time to honor the patients, families, caregivers, and healthcare professionals who are part of the rare disease community. At PacBio, we are passionate about supporting this community and providing tools that help improve the ability of scientists and clinicians to deliver valuable answers to families and reduce what can be a years-long diagnostic odyssey. And while each ‘rare’ disease may affect a limited number of people, collectively these diseases affect hundreds of millions of people around the world. Since we last celebrated this special day, we’ve been particularly excited by the progress made…
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…
This blog post has been updated, it was originally published September 2016. In recent interactions with the scientific community, we’ve seen a growing number of questions around scaffolding genome assemblies. We thought it might be useful to review the concepts behind contigs and scaffolds, as well as the circumstances in which one might want to scaffold a high-quality PacBio genome assembly. Contigs vs. Scaffolds Contigs are continuous stretches of sequence containing only A, C, G, or T bases without gaps. SMRT Sequencing has all of the necessary performance characteristics – long reads, lack of sequence-context bias, and high accuracy –…
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…
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…
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…
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…
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,…
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…