The Genome in a Bottle (GIAB) consortium performs authoritative characterization of 7 human genomes. Here, we describe work towards generating a new GIAB small variant benchmark that incorporates long and linked read sequencing data. The GIAB …
Introduction: Long-read PacBio SMRT Sequencing has been applied successfully to assemble genomes and detect structural variants. However, due to high raw read error rates of 10-15%, it has remained difficult to call small variants from long reads. …
Bipolar disorder (BD) is a phenotypically and genetically complex neurological disorder that affects 1% of the worldwide population. There is compelling evidence from family, twin and adoption studies supporting the involvement of a genetic …
Introduction: Long-read sequencing has been applied successfully to assemble genomes and detect structural variants. However, due to high raw-read error rates (10-15%), it has remained difficult to call small variants from long reads. Recent …
Introduction: Long-read sequencing has been applied successfully to assemble genomes and detect structural variants. However, due to high raw-read error rates (10-15%), it has remained difficult to call small variants from long reads. Recent …
Background: Cancer is caused by somatic DNA alterations, which comprise small nucleotide variants (SNVs), chromosome somatic copy number alterations (SCNAs) and chromosomal breakpoint structural variants (SVs). Previously, we investigated …
Recent improvements in sequencing chemistry and instrument performance combine to create a new PacBio data type, Single Molecule High-Fidelity reads (HiFi reads). Increased read length and improvement in library construction enables average read …
Human genomic variation ranges in size from single nucleotide substitutions to large chromosomal rearrangements. Sequencing technologies tend to be optimized for detecting particular variant types and sizes. Short reads excel at detecting SNVs and …
Incomplete annotation of genomes represents a major impediment to understanding biological processes, functional differences between species, and their evolutionary mechanisms. Often, genes that are large, embedded within duplicated genomic regions, …
Mitochondrial DNA (MtDNA) mutations have been increasingly recognized as important contributors to an array of human diseases such as Parkinson’s disease, Alzheimer’s disease, colorectal cancer, and Kearns–Sayre syndrome. Characterization of the …