Seven years after the ALS Ice Bucket Challenge soaked the world, the pace of discovery in sporadic amyotrophic lateral sclerosis has increased tremendously, with more than $115 million dollars in donations funding research that has led to the identification of several genes implicated in both familial and sporadic cases of the neurodegenerative disease. While the social campaigns have generated much needed awareness around the disease, there are other challenges – one of which can be addressed with long-read sequencing. As detailed in a new, interactive case study, PacBio SMRT Sequencing is helping researchers at the University of Washington unravel…
It’s a challenge that has haunted rare disease researchers for years: how to increase solve rates in rare and Mendelian disease. Currently, the genetic cause of more than half of rare disease cases worldwide remain unexplained. In a series of talks and posters presented at the 2021 annual meeting of The European Society of Human Genetics (#ESHG21), PacBio experts and users described how HiFi sequencing could help close the gap by providing more comprehensive, accurate and high-definition coverage of the gaps in the human genome. Here is a summary of the discussions that took place and the posters that…
It’s a moment three decades in the making: the first complete human genome assembly is here! Reading this you will no doubt feel some sense of déjà vu. After all, the human genome reference was pronounced “done” in 2000, 2001, and again in 2003. But any scientist who has used the reference since then knows that there has never been a single fully sequenced human genome. Until now. HiFi Sequencing Enables the First Complete Sequence of a Human Genome The Telomere-to-Telomere (T2T) Consortium, a large team of scientists from the National Human Genome Research Institute and dozens of other institutions,…
If you are like most of us at PacBio you likely learned how to extract DNA in a high school or college biology class, or maybe even in your kitchen. But as you moved on to more high stakes experiments, you may have found that extracting DNA for sequencing in your lab isn’t always as straightforward as lyse, precipitate, wash, suspend. In this introduction to DNA extraction, we will share tips, tricks, and protocols to help make your DNA isolation easier! For optimal results to power biological discovery, sample prep is a critical step in any sequencing project. And with…
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…
Today we’re pleased to announce the three winners of our latest SMRT Grant which called for teams of researchers and collaborative projects that could be addressed using the power of HiFi sequencing. The winners are seeking to solve a diverse set of questions from mussel-hopping transmissible cancer to the power of pistachios to help tackle climate change, and sex determination in bearded dragons. The 2020 HiFi for All – Collaborations SMRT Grant Program was open to scientists worldwide and offered three winning projects awards of up to 10 SMRT Cells 8M and sequencing on the Sequel II or…
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…
A pangenome identifies which portions of the genome are unique and which overlap and are therefore core to the species. It has recently become apparent how important it is to sequence more than one individual to characterize the genomic variation within a species. This makes sense if you consider that sexually reproducing organisms are a mix of their parents and, therefore, not identical. This is just as true in crops as it is in humans. So, it’s not surprising that when a group of researchers from several institutions in China embarked on de novo genome assemblies of several accessions of…
As the flurry of research around the SARS-CoV-2 virus continues at an unprecedented pace, scientists are beginning to tackle some of the more complex immunological responses with the help of Single Molecule, Real-Time (SMRT) sequencing. Hundreds of people tuned in live to a special May 7 webinar, “Understanding SARS-CoV-2 and host immune response to COVID-19 with PacBio sequencing.” Meredith Ashby, Director of Microbial Genomics at PacBio, described some of the resources being generated by both PacBio and our users in order to help labs who are using SMRT Sequencing technology to investigate SARS-CoV-2 and COVID-19. These include two microbial sequencing…
The new and updated species in Ensembl 99 from the Vertebrate Genomes Project (VGP) Meerkats, yaks, geese, and lots of flies — oh my! A full menagerie of new and updated animal genomes has been released by the Ensembl project. The Ensembl 99 release includes a variety of vertebrates, plants, mosquitos, and flies, as well as updates of human gene annotation and variation data. Among them are 38 new species and two dog breeds (Great Dane and Basenji), as well as four updated genome assemblies. Many were created using PacBio sequencing data. Thirteen of the new assemblies have…
PacBio highly accurate long reads, known as HiFi reads, offer all the benefits of long-read sequencing with accuracy comparable to short-read sequencing. To celebrate this new paradigm in sequencing technology, we hosted the 2019 HiFi for All SMRT Grant this past fall. This SMRT Grant was open to scientists worldwide and offered three winning projects each up to six SMRT Cells 8M and sequencing on the Sequel II System by our Certified Service Providers and co-sponsors. In response to our call for projects across the range of SMRT Sequencing applications, we received many truly compelling proposals, which made selecting…
The rarest day on the calendar is February 29th — which makes it the perfect time to celebrate Rare Disease Day. On this day, we join millions of people around the world making time to honor the patients, caregivers, healthcare professionals and scientists who deal with rare diseases every day. Zoe Harting was diagnosed with Type 1 SMA and was not expected to live past the age of 2, but is now reaching unprecedented milestones as an energetic 7-year-old, thanks to an experimental treatment. And we didn’t have to look far to find someone affected. Bioinformation John Harting, of our…
Launched in 1996, NARMS is a U. S. public health surveillance system that tracks antimicrobial susceptibility of select foodborne enteric bacteria. We hear a lot about the growing crisis of antibiotic resistance in human health, but it turns out this is just the most visible place it appears as it moves through our complex modern environment. For example, when intensive farming is used to feed large urban populations, antibiotic resistance can first emerge on farms and gain access to human communities through the food system. One of the key groups on the front lines of monitoring antibiotic resistance from farm…
Matt Hufford, associate professor at Iowa State University, helped produce a 26-line maize pangenome assembly collection Maize researchers have been rejoicing over a New Year’s gift delivered by a group of 33 scientists: A 26-line “pangenome” reference collection. The multi-institutional consortium of researchers used the Sequel System and BioNano Genomics optical mapping to create the assemblies and high-confidence annotations. They released the results on January 9, and in several presentations at the Plant and Animal Genome XXVIII Conference, less than two years after the ambitious project was funded by a $2.8 million National Science Foundation grant. The collection includes comprehensive,…