Asset Type: Media article
The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars
Identification of a novel 91.5 kb-deletion (αα)FJ in the α-globin gene cluster using single-molecule real-time (SMRT) sequencing
Transposable element-mediated rearrangements are prevalent in human genomes
Transposable elements constitute about half of human genomes, and their role in generating human variation through retrotransposition is broadly studied and appreciated. Structural variants mediated by transposons, which we call transposable element-mediated rearrangements (TEMRs), are less well studied, and the mechanisms leading to their formation as well as their broader impact on human diversity are poorly understood. Here, we identify 493 unique TEMRs across the genomes of three individuals. While homology directed repair is the dominant driver of TEMRs, our sequence-resolved TEMR resource allows us to identify complex inversion breakpoints, triplications or other high copy number polymorphisms, and additional complexities. TEMRs are enriched in genic loci and can create potentially important risk alleles such as a deletion in TRIM65, a known cancer biomarker and therapeutic target. These findings expand our understanding of this important class of structural variation, the mechanisms responsible for their formation, and establish them as an important driver of human diversity.
Design and performance of a long-read sequencing panel for pharmacogenomics
Pharmacogenomics (PGx)-guided drug treatment is one of the cornerstones of personalized medicine. However, the genes involved in drug response are highly complex and known to carry many (rare) variants. Current technologies (short-read sequencing and SNP panels) are limited in their ability to resolve these genes and characterize all variants. Moreover, these technologies cannot always phase variants to their allele of origin. Recent advance in long-read sequencing technologies have shown promise in resolving these problems. Here we present a long-read sequencing panel-based approach for PGx using PacBio HiFi sequencing.
Clinical NGS
PacBio CSO Jonas Korlach discusses the implications for SMRT Sequencing in clinical research.
SMALR Bacterial Epigenetics
Researchers have reported an important advance for using SMRT sequencing for epigenetic studies with a new approach capable of probing epigenetic heterogeneity in a population of seemingly identical bacteria.
Following Feasibility Study, UK Registry Plans to Implement PacBio for HLA Typing by Year’s End
GenomeWeb: The UK’s Anthony Nolan Research Institute plans to start using Pacific Biosciences’ sequencing technology routinely for HLA typing by the end of this year after scientists from the institute and PacBio published a feasibility study this spring.
Clone-Free, Single-Molecule Genome Assembly Illuminates Structural Variation
A team of scientists has published one of the most detailed explorations to date of complex structural variation in a human genome. The results highlight just how much genomic variation is missed when working exclusively with short-read sequencing technologies.
Human Genome Sequenced without Cloning Steps
A collaboration of scientists led by researchers from Icahn School of Medicine at Mt. Sinai has created a comprehensive analysis of a diploid human genome using two complementary single DNA molecule methods for sequencing and genome mapping, and without the need for any DNA amplification techniques.
PacBio Explores Targeted Sequencing, Focusing on Complex Genomic Regions
Pacific Biosciences is making advances in the targeted sequencing space, including a partnership with Roche NimbleGen.
PacBio, RainDance Technologies Partner to Commercialize Whole-Genome Assembly Solution
The approach should allow “haplotype phas[ing] and assembly of complex regions even in genomic regions containing complex repeats or PCR-challenged sequences that limit the performance of other synthetic long read approaches based on short read sequencing technologies”.
PacBio, RainDance to Co-Develop De Novo Whole Genome Assembly Product
These solutions will combine the power of RainDance’s proprietary digital droplet technology and single-molecule barcoding capabilities with Pacific Biosciences’ proprietary long-range DNA amplification technology to provide sample preparation upstream of PacBio’s long-read sequencing system.
Tapping the Yeast Genome
Cover Story – Researchers are bringing advanced technologies like SMRT Sequencing to improve the ancient art of beer brewing.
Baylor Team Aims for ‘Gold Standard’ in Structural Variant Calling
Researchers from Baylor College of Medicine reported in BMC Genomics how they employed multiple sequencing technologies, library preparations, assembly methods, and genome mapping tools to work toward creating a reference diploid genome long read data from PacBio was especially important.