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…
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…
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…
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…
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…
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…
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…
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…
As the world faces an unprecedented pandemic caused by a novel coronavirus, the scientific spotlight has shone brightly on infectious disease research. And although interest in Public Health England’s (PHE) Culture Collections is often focused on its historical cultures, its relevance in our modern world has never seemed sharper. The National Collection of Pathogenic Viruses (NCPV) has been helping scientists from around the world address the current history-making infectious disease event. It is also anticipating future outbreaks, and building collections of pathogenic viruses to aid research into potential threats to human health. “The question of which virus will be next…
The new Sequel IIe System provides direct access to HiFi sequencing Still soaring from the success of last year’s launch of the award-winning Sequel II System, we’re excited to announce the next evolution of the instrument: the Sequel IIe System. This evolution includes increased computing power and advanced on-instrument data processing. This means the instrument can directly produce the widely coveted, highly accurate long reads, known as HiFi reads, that have made the original Sequel II System indispensable for many labs — and save users time and money in the process. Just how much of an improvement does the new…
Nearly gapless, reference-quality chromosome-level assemblies — in less than a day? Yes, it’s possible, thanks to the high accuracy and low computational needs of PacBio HiFi reads. Kevin Fengler, computational genomics lead at Corteva Agriscience, welcomed watchers to the brave new world of the pangenome during the recent webinar, “Beyond a Single Reference Genome – The Advantages of Sequencing Multiple Individuals.” We are now living in an era where you can generate a reference genome assembly that’s specific for each application or trait of interest, Fengler said. Graphic alignment of dozens of genomes in a pangenome collection allows researchers to…
Even in the field of genomics where new breakthroughs occur every few months, completion of the first-ever fully sequenced human autosome is a momentous achievement. Highly accurate, no gaps, no mis-joins — just chromosome 8 in all its glory. It’s a remarkable feat and we are honored that PacBio HiFi reads played a pivotal role in helping to achieve it. The complete centromere sequence of chromosome 8 shows a diversity of satellite repeats and other abundant genomic repeats, now with near perfect base-level resolution from end to end. Logsdon, G et al. (2020) This work is described in a preprint…
Analysis of 16S ribosomal RNA has been used for phylogenetics and identifying prokaryotes for decades. But just as scientists have had to refine the Linnaean taxonomy system based on genomic discoveries, improvements in sequencing technology are changing 16S analysis best practices. Several dominant microbial genera in Sakinaw Lake could only be resolved via Full Length 16S or were missed by V4 sequencing (gray boxes). Singer, E. et al. (2016) Researchers at the Joint Genome Institute, for instance, conducted a detailed benchmarking study and found that traditional methods of 16S analysis — which look at just a piece of the gene…
The SMRTbell gDNA Sample Amplification Kit enables whole genome amplification starting from as little as 5 ng of genomic DNA. It’s one of the questions we hear most often from scientists working with small organisms: Is it possible to generate truly high-quality, long-read data from minuscule amounts of DNA? With our new kit for ultra-low DNA input projects, the answer is: Absolutely! The new workflow dramatically reduces the requirements for DNA quantity. Now, scientists need only 5 ng of genomic DNA to kick off a SMRT Sequencing project — that’s less than 2% of the starting volume needed for our…
With PacBio HiFi sequencing data now readily available for organisms of any size, many exciting results have been published featuring new de novo assembly methods optimized for highly accurate long reads. These methods have produced assemblies for a variety of organisms at quality levels never before thought possible — as measured by completeness, contiguity and correctness. We feel privileged to collaborate with the scientific community on the development of these tools. From Small to Tall When the USDA wanted to rapidly assemble the Asian Giant Hornet as part of its real-time invasive species response initiative, they turned to a tool…