Structural variation accounts for much of the variation among human genomes. Structural variants of all types are known to cause Mendelian disease and contribute to complex disease. Learn how long-read sequencing is enabling detection of the full spectrum of structural variants to advance the study of human disease, evolution and genetic diversity.
Explore how long-read sequencing enables solving of rare and mendelian diseases.
PacBio HiFi reads (minimum 99% accuracy, 15-25 kb read length) have emerged as a powerful data type for comprehensive variant detection in human genomes. The HiFi read length extends confident mapping and variant calling to repetitive regions of the genome that are not accessible with short reads. Read length also improves detection of structural variants (SVs), with recall exceeding that of short reads by over 30%. High read quality allows for accurate single nucleotide variant and small indel detection, with precision and recall matching that of short reads. While many tools have been developed to take advantage of these qualities…
Melissa Laird Smith discussed how the Icahn School of Medicine at Mount Sinai uses long-read sequencing for translational research. She gave several examples of targeted sequencing projects run on the Sequel System including CYP2D6, phased mutations of GLA in Fabry’s disease, structural variation breakpoint validation in glioblastoma, and full-length immune profiling of TCR sequences.
Howard Jacob, Chief Genomics Officer at the HudsonAlpha Institute for Biotechnology, explored the role of genomics in diagnosing rare diseases. In this podcast he shared his views on the economics of clinical sequencing and how long-read sequencing is advancing the ability to sequence an individual’s genome –de novo– and use structural variant calling to make clinical diagnoses. He concluded with the hurdles limiting adoption of clinical sequencing and his vision for the future of genomic medicine.
In this webinar we present Single Molecule, Real-Time (SMRT) Sequencing and the Iso-Seq method, which allow you to generate full-length cDNA sequences — no assembly required — to characterize transcript isoforms within targeted genes or across an entire transcriptome. The presenters share how the Iso-Seq method: (1) Provides high quality, full-length transcript sequences of up to 15 kb; (2) Allows for one-day library prep on a single SMRT Cell 8M to comprehensively characterize a whole transcriptome; (3) Facilitates discovery of alternative splicing events, fusion gene detection, and allelic specific isoform detection; and (4) Enables discovery of potential cancer-specific isoforms in…
The problem of ‘missing heritability’ affects both common and rare diseases hindering: discovery, diagnosis, and patient care. The ‘missing heritability’ concept has been mainly associated with common and complex diseases where promising modern technological advances, like genome-wide association studies (GWAS), were unable to uncover the complete genetic mechanism of the disease/trait. Although rare diseases (RDs) have low prevalence individually, collectively they are common. Furthermore, multi-level genetic and phenotypic complexity when combined with the individual rarity of these conditions poses an important challenge in the quest to identify causative genetic changes in RD patients. In recent years, high throughput sequencing has…
Current programmable nuclease-based methods (for example, CRISPR-Cas9) for the precise correction of a disease-causing genetic mutation harness the homology-directed repair pathway. However, this repair process requires the co-delivery of an exogenous DNA donor to recode the sequence and can be inefficient in many cell types. Here we show that disease-causing frameshift mutations that result from microduplications can be efficiently reverted to the wild-type sequence simply by generating a DNA double-stranded break near the centre of the duplication. We demonstrate this in patient-derived cell lines for two diseases: limb-girdle muscular dystrophy type 2G (LGMD2G)1 and Hermansky-Pudlak syndrome type 1 (HPS1)2. Clonal…