Structural variation

deCODE genetics - Rounding off the human genome

Retrieved on: 
Monday, May 10, 2021
Branches of biology, Biology, Genetics, Biotechnology, Molecular biology, Genomics, DNA, deCODE genetics, Whole genome sequencing, Read, Third-generation sequencing, Structural variation

However of 133,886 reliably genotyped structural variants detected with long-read sequencing only 60% can be detected with short-reads.\nUsing PromethION sequencers from Oxford Nanopore Technologies, researchers at deCODE genetics whole genome sequenced 3,622 Icelanders.

Key Points: 
  • However of 133,886 reliably genotyped structural variants detected with long-read sequencing only 60% can be detected with short-reads.\nUsing PromethION sequencers from Oxford Nanopore Technologies, researchers at deCODE genetics whole genome sequenced 3,622 Icelanders.
  • These variants were then imputed into a larger set of participants in various disease studies at deCODE genetics and associated with phenotypes.
  • This is a major stumbling block in the attempt to fully understand the relationship between variation in the sequence of the human genome and human diversity.
  • Using its unique expertise and population resources, deCODE has discovered genetic risk factors for dozens of common diseases.

deCODE genetics - Rounding off the human genome

Retrieved on: 
Monday, May 10, 2021
Branches of biology, Biology, Genetics, Biotechnology, Molecular biology, Genomics, DNA, deCODE genetics, Whole genome sequencing, Read, Third-generation sequencing, Structural variation

However of 133,886 reliably genotyped structural variants detected with long-read sequencing only 60% can be detected with short-reads.\nUsing PromethION sequencers from Oxford Nanopore Technologies, researchers at deCODE genetics whole genome sequenced 3,622 Icelanders.

Key Points: 
  • However of 133,886 reliably genotyped structural variants detected with long-read sequencing only 60% can be detected with short-reads.\nUsing PromethION sequencers from Oxford Nanopore Technologies, researchers at deCODE genetics whole genome sequenced 3,622 Icelanders.
  • These variants were then imputed into a larger set of participants in various disease studies at deCODE genetics and associated with phenotypes.
  • This is a major stumbling block in the attempt to fully understand the relationship between variation in the sequence of the human genome and human diversity.
  • Using its unique expertise and population resources, deCODE has discovered genetic risk factors for dozens of common diseases.

COVID-19 Host Genome SV Consortium Identifies Structural Variants with Possible Roles in Pathogenesis and Outcomes in Severely Ill COVID-19 Patients Using Bionano’s Saphyr® System

Retrieved on: 
Monday, January 11, 2021
Branches of biology, Genetics, Genomics, Genome, Personal genomics, Structural variation

The study found that optical genome mapping (OGM) with Bionanos Saphyr System identified structural variants (SVs) that affect genes in pathways that control immune and inflammatory response, viral reproduction and mucosal function.

Key Points: 
  • The study found that optical genome mapping (OGM) with Bionanos Saphyr System identified structural variants (SVs) that affect genes in pathways that control immune and inflammatory response, viral reproduction and mucosal function.
  • The authors believe these SVs may provide key insights into the pathogenesis of COVID-19 and outcomes in patients who become severely ill.
  • The consortium has selected OGM with the Saphyr System for genome analysis owing to Saphyrs documented performance as the leading platform for detecting these large SVs.
  • Anderson Cancer Center, Columbia University Medical Center, Virginia Commonwealth University, New York Genome Center, Harvard Medical School, and Bionano Genomics.

Bionano Genomics' Saphyr System Shown to be Indispensable for the Analysis of Certain Genetic Disease Causing Variants

Retrieved on: 
Thursday, October 15, 2020
Branches of biology, Biology, Mutation, Molecular evolution, Chromosomes, Gene duplication, Structural variation, Optical mapping, Segmental duplication on the human Y chromosome

Only Bionanos optical mapping technology can image single molecules that are so long that they span the segmental duplications.

Key Points: 
  • Only Bionanos optical mapping technology can image single molecules that are so long that they span the segmental duplications.
  • These repetitive sequences can interact with each other when sperm or eggs are created and their rearrangement can cause severe genetic disease.
  • Several novel SVs were detected for each locus, and the exact disease causing rearrangement was determined with much higher accuracy than was formerly possible without Saphyr.
  • An increasing number of studies have relied on Bionanos Saphyr system to characterize disease-causing structural variants that could not be correctly analyzed with other molecular techniques.

Bionano's Saphyr Plays Essential Role in Identifying Three Previously Unknown Genetic Mutation Types in Cancer in Study from Weill Cornell

Retrieved on: 
Thursday, October 8, 2020
Branches of biology, Biology, Biotechnology, Biomarker, DNA sequencing, Structural variation, Personalized onco-genomics, Cancer pharmacogenomics

The study identified three new distinct classes of structural variations (SVs) in the DNA of thousands of cancer samples across multiple cancer types, and used Saphyr to characterize the precise structure and genomic location of these variations.

Key Points: 
  • The study identified three new distinct classes of structural variations (SVs) in the DNA of thousands of cancer samples across multiple cancer types, and used Saphyr to characterize the precise structure and genomic location of these variations.
  • These previously unknown types of complex rearrangements help explain different mechanisms that enable cancer cells to expand and grow rapidly while simultaneously evading natural defense mechanisms and treatment.
  • With the addition of Bionanos Saphyr data, the study demonstrated that these structural variants generate a large number of fusion proteins and represent therapeutic targets and/or prognostic biomarkers of disease progression.
  • While cancer genomes traditionally have been studied with a combination of low-resolution cytogenetic methods or with next-generation sequencing (NGS), Bionanos Saphyr instrument provides long-range data that enables a high-resolution, long-range view into the cancer genome and cancer biology.

Boston Children’s Hospital Is Using Bionano’s Saphyr To Study Children With Severe COVID-19 Disease

Retrieved on: 
Monday, October 5, 2020
Branches of biology, Genetics, American television series, Genomics, Childrens Hospital, Genome, Structural variation

The team at Boston Childrens Hospital is using Saphyr to study the genomes of affected children and controls with the hope of identifying genomic variants that predispose to or protect against the disease, which could guide the treatment decisions made and help steer the development or use of therapeutics and/or vaccines.

Key Points: 
  • The team at Boston Childrens Hospital is using Saphyr to study the genomes of affected children and controls with the hope of identifying genomic variants that predispose to or protect against the disease, which could guide the treatment decisions made and help steer the development or use of therapeutics and/or vaccines.
  • The Boston Childrens team has joined the COVID-19 Host Genome Structural Variation Consortium, which aims to identify structural differences in the genomes of patients affected by or protected against COVID-19.
  • The samples are currently being recruited from patients who are treated at Boston Childrens Hospital, and analyzed on the Saphyr system operated by the Molecular Genetics Core Facility of Boston Childrens Hospital.
  • Boston Childrens Hospital is ranked the #1 childrens hospital in the nation byU.S.

German Accreditation of Laboratory Developed Tests on Bionano’s Saphyr System Accelerates Utilization in Clinical Diagnostics

Retrieved on: 
Thursday, September 24, 2020
Branches of biology, Genetics, Biology, Chromosomes, Cytogenetics, Chromosomal abnormalities, Structural variation, Gene duplication, Chromosomal translocation, Accreditation, Chromosomal inversion, MVZ

The approval accredits LDTs developed by MVZ Martinsried for the detection of the following types of structural variants (SVs): translocations, inversions and duplications.

Key Points: 
  • The approval accredits LDTs developed by MVZ Martinsried for the detection of the following types of structural variants (SVs): translocations, inversions and duplications.
  • Inversions and duplications are also often implicated in cancers and all three types are known to occur in constitutional genetic disorders.
  • "MVZ Martinsrieds receipt of this first European accreditation for use of Saphyr-based LDTs is an important milestone towards broader accreditation and adoption across Europe and other regions.
  • Achieving this accreditation in Germany, the largest market in Europe, is also significant because the German accreditation process follows a very high standard," said Erik Holmlin, chief executive officer of Bionano Genomics.

Metastatic Lung Cancer Study Finds That Bionano’s Saphyr Outperforms NGS for the Detection of Structural Variants

Retrieved on: 
Monday, August 3, 2020
Branches of biology, Biology, Genetics, Chromosomes, Structural variation, Molecular biology, Biotechnology, Medical genetics

The study showed that Saphyr outperformed NGS-based methods in the detection of structural variants to characterize the genetic heterogeneity between the primary tumor and the matched metastases.

Key Points: 
  • The study showed that Saphyr outperformed NGS-based methods in the detection of structural variants to characterize the genetic heterogeneity between the primary tumor and the matched metastases.
  • Of 1026 large SVs detected on average by Saphyr in each of the tumor types, the NGS-based methods failed to detect an average of 77%.
  • Saphyr identified 52 SVs shared between the metastases, while no shared SVs were found by NGS-based methods.
  • The study authors stated that Saphyr is more capable of detecting large and complex SVs, without the computational and bioinformatic challenges that come with SV calling from NGS data.

Bionano Genomics Reports Second Quarter 2019 Financial Results and Provides Business Update

Retrieved on: 
Thursday, August 8, 2019
Branches of biology, Genetics, Biology, Genomics, Genome, Structural variation, Genetic variation, Personal genomics

SAN DIEGO, Aug. 08, 2019 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (NASDAQ: BNGO), a life sciences instrumentation company that develops and markets Saphyr, a platform for ultra-sensitive and ultra-specific structural variation detection in genome analysis, today reported its financial results for the second quarter and six-months ended June 30, 2019 and provided a business update.

Key Points: 
  • SAN DIEGO, Aug. 08, 2019 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (NASDAQ: BNGO), a life sciences instrumentation company that develops and markets Saphyr, a platform for ultra-sensitive and ultra-specific structural variation detection in genome analysis, today reported its financial results for the second quarter and six-months ended June 30, 2019 and provided a business update.
  • Presented initial results from key clinical studies designed to evaluate the performance of Saphyr against traditional cytogenetics methods at the European Human Genetics Conference.
  • We are pleased to make progress each quarter on our goal of establishing Saphyr as a best-in-class structural variation detection and discovery system, said Erik Holmlin, Ph.D., CEO of Bionano.
  • The Company will host a conference call and live webcast to discuss its second quarter 2019 financial results and provide an update on business activities.