• Application

  • Implementation

Publications

Molecular and Cellular Endocrinology 2018
Barseghyan H et al
Genome Research 2017
McCaffrey J et al
Genome Research (2014); 24: 2066-2076 
Steinberg, K. et al.
BioMed Central Genomics (2014); 15(July 2014): 387 
O’Bleness, M., et al.

Videos

Unraveling complex structural variant patterns in cancer using optical mapping...
Towards high quality reference assemblies for all vertebrate genomes
Bionano data solutions to power your next discovery
Identifying structure of human papillomavirus genomes in head and neck...
Bionano optical mapping, in combination with other sequencing-based technologies, to...
Reference quality genomes of bats to illuminate the genomic determinants...
Improvements of North American catfish genome assemblies with optical mapping.
Recent workflow advances from Bionano Genomics
Genomic insights revealed by optical mapping the 3q29 deletion interval
Uncovering the precise genomic location of inversion events using optical...
Going beyond a single human reference. Lessons learned from sequencing...
Applications of whole genome imaging in translational research
Making the right call for structural variants interpretation using artificial...
Bionano mapping for evaluation of structural variants in genetic diseases
Optical mapping for chromosomal abnormalities. A pilot study for feasibility...
Characterization of clinically relevant repeats in the human genome
A novel molecular diagnostic tool for comprehensive assessment of structural...
Whole genome imaging to streamline cancer cytogenetics and identify novel...
High resolution view of D4Z4 repeat regions for studying FSHD...
Advanced analysis of risk loci in congenital disorders using Bionano...
Resolving complex genomic haplotypes in neurodegenerative disorders using Bionano Genomics...
Dr. Sven Bocklandt details the Saphyr Genome Imaging System's SV...
Dr. Hoischen reviews his work using Bionano digital cytogenetics applications
Dr. Kanagal-Shamanna shares how Saphyr technology detected novel structural variants...
Dr. Brynn Levy shares how Saphyr technology accurately detected clinical...
Overview of Bionano’s whole genome imaging technology.
Dr. Hastie reviews Bionano Saphyr's genome assembly capabilities at the...
Dr. Bocklandt reviews new developments in Bionano optical mapping and...
Dr. El Khattabi discusses Saphyr's ability to detect balanced and...
Dr. Hoischen discusses the assessment of Bionano Saphyr as a...

Webinars

Accurate analysis of structural variants begins with isolating ultra-high molecular weight DNA. Obtaining high-quality UHMW DNA can present a challenge since sample collection, preservation, the DNA isolation process and subsequent handling of isolated DNA can significantly affect its quality.

In this webinar, Dr. Ben Clifford, Sr. Application Scientist at Bionano Genomics, discusses tips and tricks for isolating high quality UHMW DNA – right from sample collection, preservation and gentle handling of isolated DNA to minimize shearing and fragmentation.

In addition, we heard from Dr. Sven Bocklandt, Director of Scientific affairs at Bionano Genomics to walk us through genome imaging technology and workflow to demonstrate how it has been used successfully in studying structural variations in cancer and genetic diseases.

Cordelier Research Center - Paris
Dr. Eric Letouzé

“Bionano’s optical mapping technology allowed us to characterize complex structural rearrangements in cancer with unprecedented precision. The results are incredibly robust and easy to interpret with Bionano software, and the team was really helpful for data analysis!”
-Dr. Eric Letouzé

Cyclins A2 and E1 regulate the cell cycle by promoting S phase entry and progression. We recently identified a hepatocellular carcinoma (HCC) subgroup exhibiting cyclin activation through various mechanisms, including HBV and AAV2 viral insertions, gene fusions and enhancer hijacking. Those poor-prognosis HCCs display a unique signature of structural rearrangements, triggered by replicative stress. This signature is strongly enriched in early-replicated active chromatin regions and is characterized by hundreds of tandem duplications and more complex events called Templated Insertion Cycle (T.I.C.).

Structural variation calling from short-read Whole Genome Sequencing provides abnormal junctions by comparing chimeric reads with a reference genome. However, those independent breakpoints are too distant, thus this method is not enough to reconstruct highly complex rearrangements, which may involve up to dozens of regions of the genome linked together. Here we used Bionano data to characterize with certainty large DNA molecules resulting from complex T.I.C.. This analysis allowed us to know which regions of the genome are the acceptor of such complex structural rearrangements. This information is critical in the understanding of how those rearrangements affect genes involved in tumorigenesis by placing oncogenes in different genomic contexts.

Sanford Burnham Prebys Medical Discovery Institute
Dr. Darren "Ben" Finlay & Dr. Rabi Murad
Sanford Burnham Prebys Medical Discovery Institute
Dr. Darren "Ben" Finlay & Dr. Rabi Murad
Bionano Genomics
Dr. Sven Bocklandt

Accumulation of structural variations (SVs) across the genome is a known trigger factor for oncogenesis. Identifying these structural genomic alterations – accurately and comprehensively – is crucial for improving research and ultimately therapies for cancer patients, yet one of primary challenges when solely relied on short read sequencing and standard cytogenetic methods (e.g. karyotyping, FISH and chromosomal microarrays).

Optical mapping with genome imaging, enabled by the Bionano Saphyr® System, can accurately assemble and assay relevant regions for complex genomic disorders like cancer, even those involving very large segmental duplications. Genome imaging has to date unraveled a number of genes, never implicated in cancer and shown how they are affected by structural variations, along with deciphering novel structural variants. Listen to this webinar to learn how combining genome imaging with whole genome sequencing offers a strong integrative approach to understand small and large genomic variations in cancers.

Radbound Medical Center
Dr. Alexander Hoischen, Associate Professor, Genomic Technologies & Immuno-genomics

This webinar outlines how a team at Radboud University Medical Center is assessing ultra-long read optical mapping on the Bionano Saphyr System to replace classical cytogenetics approaches in routine testing and for the discovery of novel structural variants with potential scientific, prognostic, or therapeutic value that are missed by standard approaches.

Vanessa Hayes
Garvan Institute of Medical Research
Dr. Vanessa Hayes, PhD
Eric Vilain
Chief of Medical Genetics at UCLA
Dr. Eric Vilain, MD, PhD
Alex Harkess
Donald Danforth Plant Science Center
Alex Harkess
Florian Jupe
Salk Institute of Biological Studies
Florian Jupe
Wellcome Trust Sanger Institute
William Chow
Kansas State University
Dr. Sue Brown
Wageningen University
Dr. Gabino Sanchez Perez
Icahn School of Medicine at Mount Sinai
Dr. Ali Bashir and Dr. Bobby Sebra
The Genome Institute at Washington University
Tina Graves
Institute of Experimental Botany, Olomouc
Dr. Jaroslav Dolezel
Emory University
Dr. Michael Rossi

Posters

February, 2020
AGBT 2020, Marco Island, Florida
February, 2018
Advances in Genome Biology and Technology, Orlando, Fl
February, 2018
Advances in Genome Biology and Technology, Orlando, Fl
May, 2017
European Society of Human Genetics Annual Meeting, Copenhagen, Denmark
May, 2017
European Society of Human Genetics Annual Meeting, Copenhagen, Denmark
March, 2017
ACMG Annual Clinical Genetics Meeting, Phoenix, Arizona
February, 2017
Advances in Genome Biology and Technology 2017 General Meeting, Hollywood, FL
February, 2017
Advances in Genome Biology and Technology 2017 General Meeting, Hollywood, FL
January, 2017
Plant and Animal Genome Conference XXV, San Diego, CA
January, 2017
Plant and Animal Genome Conference XXV, San Diego, CA
October, 2016
American Society of Human Genetics, San Diego, CA
March, 2016
Annual Clinical Genetics Meeting, Tampa, FL
February, 2016
Advances in Genome Biology and Technology, Orlando, FL
February, 2016
Advances in Genome Biology and Technology, Orlando, FL
January, 2016
Plant and Animal Genome Conference XVII, San Diego, CA
January, 2016
Plant and Animal Genome Conference XVII, San Diego, CA
January, 2016
Plant and Animal Genome Conference XVII, San Diego, CA
January, 2016
Plant and Animal Genome Conference XVII, San Diego, CA
January, 2016
Plant and Animal Genome Conference XVII, San Diego, CA
October, 2015
American Society of Human Genetics, Baltimore, MD
October, 2015
American Society of Human Genetics, Baltimore, MD
October, 2015
American Society of Human Genetics, Baltimore, MD
October, 2015
American Society of Human Genetics, Baltimore, MD
October, 2015
American Society of Human Genetics, Baltimore, MD
May 2015 / June 2015
Biology of Genomes / European Society of Human Genetics, Cold Spring Harbor, NY (USA) / Glasgow (UK)
May 2015 / June 2015
Biology of Genomes / European Society of Human Genetics, Cold Spring Harbor, NY (USA) / Glasgow (UK)
May 2015 / June 2015
Biology of Genomes / European Society of Human Genetics, Cold Spring Harbor, NY (USA) / Glasgow (UK)
April 2015 / June 2015
American Association for Cancer Research / European Society of Human Genetics, Philadelphia, PA (USA) / Glasgow (UK)
February, 2015
Advances in Genome Biology and Technology, Marco Island, FL
February, 2015
Advances in Genome Biology and Technology, Marco Island, FL
February, 2015
Advances in Genome Biology and Technology, Marco Island, FL
January, 2015
Plant and Animal Genome XXIII, San Diego, CA
January, 2015
Plant and Animal Genome XXIII, San Diego, CA
January, 2015
Plant and Animal Genome XXIII, San Diego, CA
November, 2014
Precision Medicine: Personal Genomes & Pharmacogenomics, Cold Spring Harbor, NY
October, 2014
Beyond the Genome, Boston, MA
October, 2014
American Society of Human Genetics, San Diego, CA
October, 2014
American Society of Human Genetics, San Diego, CA
October, 2014
American Society of Human Genetics, San Diego, CA
October, 2014
American Society of Human Genetics, San Diego, CA
September, 2014
Human Genome Variation, Belfast, Ireland
June, 2014
European Society of Human Genetics, Milan, Italy
June, 2014
European Society of Human Genetics, Milan, Italy
May, 2014
Sequencing, Finishing, Analysis in the Future, Santa Fe, NM
May, 2014
Sequencing, Finishing, Analysis in the Future, Santa Fe, NM
February, 2014
Advances in Genome Biology and Technology, Marco Island, FL
January, 2014
Plant and Animal Genome Conference XVII, San Diego, CA
November, 2013
Precision Medicine: Personal Genomes & Pharmacogenomics, Cold Spring Harbor, NY
January, 2013
Plant and Animal Genome Conference XXI, San Diego, CA
November, 2012
American Society of Human Genetics, San Francisco, CA

Literature

white papers

This white paper is based on a webinar presentation by Alexander Hoischen of Radboud University Medical Center, in which he discussed the promise of genome imaging technology for medical genetics.

Dr. Hoischen shared details of a proof-of-concept study his lab is conducting to evaluate the Saphyr whole genome imaging technology from Bionano Genomics as a possible replacement for karyotyping, fluorescent in situ hybridization, and copy number variant microarrays.

white papers

This White Paper explains how NGS leaves half of patients with genetic disorders without a molecular diagnosis, because it fails to adequately analyze repetitive parts of the genome and large structural variation. Bionano Genome Imaging is able to detect all SV types with high sensitivity and specificity, and examples of cancer and genetic disease are shown.

white papers

This white paper is based on a webinar presentation by Dr. James Broach of the Penn State College of Medicine. He discussed methods for capturing a comprehensive snapshot of all variants—both point mutations and structural variants—present in a tumor sample in order to gain insights about the genetic and genomic basis of individual cancers.

white papers

Bionano whole genome imaging is the only technology that allows for the highly sensitive detection of all structural variant types present at low allele fraction in heterogenous cancer samples, in an unbiased genome-wide manner. By providing a complete and unambiguous picture of the cancer genome structure, it can identify prognostic markers not currently monitored, and enable a complete characterization of the cancer genome in single test, potentially replacing multiple cytogenetic tests that make up the gold standard.

white papers

This white paper explains how Bionano whole genome imaging can make any sequence assembly up to 100 times more contiguous by scaffolding sequence contigs, and more exact by correcting errors. The new two-enzyme hybrid scaffold pipeline introduced here improves both aspects. It creates functional genomes at a low cost, no matter what your sequencing strategy is.

case studies

This Case Study demonstrates the power of combining 2 single molecule technologies to produce Gold-quality genomes. Those allow the discovery of substantial amount of structural variation unique to individuals and populations otherwise not accessed by other short-read technologies.

case studies

This Case Study highlights Scientists at the USDA and Cold Spring Harbor Laboratory who know that better breeding of maize to feed a growing population will depend on an accurate reference assembly. They tackled the previously intractable crop with a combination of PacBio® Sequencing and BioNano Genomics®genome maps, leading to the first-ever high-quality reference assembly.

case studies

Scientists at Rutgers University, Washington University, and Ibis Biosciences successfully deployed Next-Generation Mapping (NGM) technology from Bionano Genomics to help produce the first complete assembly for a fast-growing aquatic plant with biofuel potential. What emerged is a clear view into a genome undergoing drastic reduction and a tool to elucidate chromosome-scale dynamics.