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April 23, 2019

Application Brief: Structural variant detection using whole genome sequencing – Best Practices

With the Sequel II System powered by Single Molecule, Real-Time (SMRT) Sequencing technology and SMRT Link v7.0, you can affordably and effectively detect structural variants (SVs), copy number variants, and large indels ranging in size from tens to thousands of base pairs. PacBio long-read whole genome sequencing comprehensively resolves variants in an individual with high precision and recall. For population genetics and pedigree studies, joint calling powers rapid discovery of common variants within a sample cohort.

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April 23, 2019

Application Brief: Variant detection using whole genome sequencing with HiFi reads – Best Practices

With highly accurate long reads (HiFi reads) from the Sequel II System, powered by Single Molecule, Real-Time (SMRT) Sequencing technology, you can comprehensively detect variants in a human genome. HiFi reads provide high precision and recall for single nucleotide variants (SNVs), indels, structural variants (SVs), and copy number variants (CNVs), including in difficult-to-map repetitive regions.

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October 16, 2018

Improving the reference with a diversity panel of sequence-resolved structural variation

Although the accuracy of the human reference genome is critical for basic and clinical research, structural variants (SVs) have been difficult to assess because data capable of resolving them have been limited. To address potential bias, we sequenced a diversity panel of nine human genomes to high depth using long-read, single-molecule, real-time sequencing data. Systematically identifying and merging SVs =50 bp in length for these nine and one public genome yielded 83,909 sequence-resolved insertions, deletions, and inversions. Among these, 2,839 (2.0 Mbp) are shared among all discovery genomes with an additional 13,349 (6.9 Mbp) present in the majority of humans,…

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March 8, 2018

Webinar: Sequencing structural variants for disease gene discovery and population genetics

Structural variants (SVs, differences >50 base pairs) account for most of the base pairs that differ between two human genomes, and are known to cause over 1,000 genetic disorders including ALS, schizophrenia, and hereditary cancer. Yet, SVs remain overlooked in human genetic research studies due to the limited power of short-read sequencing methods (exome and whole genome sequencing) to resolve large variants, which often involve repetitive DNA. Recent advances in long-read sequencing have made it possible to detect the over 20,000 SVs that are now known to exist in a human genome. Corresponding advances in long-read SV calling algorithms have…

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January 22, 2018

Cytogenomic identification and long-read single molecule real-time (SMRT) sequencing of a Bardet-Biedl Syndrome 9 (BBS9) deletion.

Bardet-Biedl syndrome (BBS) is a recessive disorder characterized by heterogeneous clinical manifestations, including truncal obesity, rod-cone dystrophy, renal anomalies, postaxial polydactyly, and variable developmental delays. At least 20 genes have been implicated in BBS, and all are involved in primary cilia function. We report a 1-year-old male child from Guyana with obesity, postaxial polydactyly on his right foot, hypotonia, ophthalmologic abnormalities, and developmental delay, which together indicated a clinical diagnosis of BBS. Clinical chromosomal microarray (CMA) testing and high-throughput BBS gene panel sequencing detected a homozygous 7p14.3 deletion of exons 1-4 of BBS9 that was encompassed by a 17.5?Mb region…

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January 1, 2018

Somatic second hit mutation of RASA1 in vascular endothelial cells in capillary malformation-arteriovenous malformation.

Capillary malformation-arteriovenous malformation (CM-AVM) is an autosomal dominant vascular disorder that is associated with inherited inactivating mutations of the RASA1 gene in the majority of cases. Characteristically, patients exhibit one or more focal cutaneous CM that may occur alone or together with AVM, arteriovenous fistulas or lymphatic vessel abnormalities. The focal nature and varying presentation of lesions has led to the hypothesis that somatic "second hit" inactivating mutations of RASA1 are necessary for disease development. In this study, we examined CM from four different CM-AVM patients for the presence of somatically acquired RASA1 mutations. All four patients were shown to…

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January 1, 2018

Somatic mosaicism of an intragenic FANCB duplication in both fibroblast and peripheral blood cells observed in a Fanconi anemia patient leads to milder phenotype.

Fanconi anemia (FA) is a rare disorder characterized by congenital malformations, progressive bone marrow failure, and predisposition to cancer. Patients harboring X-linked FANCB pathogenic variants usually present with severe congenital malformations resembling VACTERL syndrome with hydrocephalus.We employed the diepoxybutane (DEB) test for FA diagnosis, arrayCGH for detection of duplication, targeted capture and next-gen sequencing for defining the duplication breakpoint, PacBio sequencing of full-length FANCB aberrant transcript, FANCD2 ubiquitination and foci formation assays for the evaluation of FANCB protein function by viral transduction of FANCB-null cells with lentiviral FANCB WT and mutant expression constructs, and droplet digital PCR for quantitation of…

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November 16, 2017

Hunting structural variants: Population by population

Until recently, most population-scale genome sequencing studies have focused on identifying single nucleotide variants (SNVs) to explore genetic differences between individuals. Like so many SNV-based genome-wide association studies, however, these efforts have had difficulty identifying causative genetic mechanisms underlying most complex functions. More and more, the genomics community has realised that structural variation is likely responsible for many of the traits and phenotypes that scientists have not been able to attribute to SNVs. This class of variants, defined as genetic differences of 50 bp or larger, accounts for most of the DNA sequence differences between any two people. Structural variants…

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November 15, 2017

Video: Structural variant detection with SMRT Sequencing

In this video, Aaron Wenger, a research scientist at PacBio, describes the use of long-read SMRT Sequencing to detect structural variants in the human genome. He shares that structural variations – such as insertions and deletions – impact human traits, cause disease, and differentiate humans from other species. Wenger highlights the use of SMRT Sequencing and structural variant calling software tools in a collaboration with Stanford University which identified a disease-causing genetic mutation.

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November 8, 2017

Podcast: Huh? 30 million Americans have a rare disease? Howard Jacob on the state of clinical sequencing

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.

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October 23, 2017

Structural variation offers new home for disease associations and gene discovery

Following completion of the Human Genome Project, most studies of human genetic variation have centered on single nucleotide polymorphisms (SNPs). SNPs are numerous in individual genomes and serve as useful genetic markers in association studies across a population. These markers have been leveraged to identify genetic loci for disease risk and draw associations with numerous traits of interest. Despite their usefulness, SNPs do not tell the whole story. For example, most SNPs are associated with only a small increased risk of disease, and they usually cannot identify on their own which genes are causal. This has resulted in what many…

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