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  • Implementation

Publications

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Long-read single-molecule maps of the functional methylome
Genome Research 2019
Sharim H et al
Genome maps across 26 human populations reveal population-specific patterns of structural variation
Nature Communications 2019
Levy-Sakin M et al
An Integrated Framework for Genome Analysis Reveals Numerous Previously Unrecognizable Structural Variants in Leukemia Patients’ Samples
2019 bioRxiv
Xu J et al
Bionano Genomics Select Publications–Human
Selected Publications Featuring Bionano Data 2019
Multiple Authors
Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements
PloS Genetics 2019
Eisfeldt J et al
Clinical application of single‐molecule optical mapping to a multigeneration FSHD1 pedigree
Molecular Genetics and Genomics Medicine 2019
Zhang Q et al
The 22q11 low copy repeats are characterized by unprecedented size and structure variability
BioRxIV 2018
Demaerel W et al
An Integrative Framework For Detecting Structural Variations In Cancer Genomes
Nature Genetics 2018
Dixon J et al
A tandem duplication of BRCA1 exons 1-19 through DHX8 exon 2 in four families with hereditary breast and ovarian cancer syndrome.
Breast Cancer Res Treat 2018
Du C et al
CRISPR-bind: a simple, custom CRISPR/dCas9-mediated labeling of genomic DNA for mapping in nanochannel arrays
bioRxIV 2018
Zhang D et al
Multi-platform discovery of haplotype-resolved structural variation in human genomes
bioRxiv 2018
Chaisson MJP et al
High-resolution comparative analysis of great ape genomes
Science 2018
Kronenber ZN et al
New technologies to uncover the molecular basis of disorders of sex development
Molecular and Cellular Endocrinology 2018
Barseghyan H et al
Optical mapping reveals a higher level of genomic architecture of chained fusions in cancer
Genome Research 2018
Eva KF Chan et al.
Single-molecule optical mapping enables accurate molecular diagnosis of facioscapulohumeral muscular dystrophy (FSHD)
BioRxIV 2018
Yi Dai et al
Reproducible integration of multiple sequencing datasets to form high-confidence SNP, indel, and reference calls for five human genome reference materials
BioRxIV 2018
Justin Zook et al
De novo assembly of two Swedish genomes reveals missing segments from the human GRCh38 reference and improves variant calling of population-scale sequencing data
BioRxIV 2018
Adam Ameur et al
Next-generation mapping: a novel approach for detection of pathogenic structural variants with a potential utility in clinical diagnosis
Genome Medicine 2017
Barseghyan H et al.
High-throughput single-molecule telomere characterization
Genome Research 2017
McCaffrey J et al
Next Generation Mapping Reveals Novel Large Genomic Rearrangements in Prostate Cancer
Oncotarget 2017
Jaratlerdsiri W et al
Ongoing human chromosome end extension driven by a primate ancestral genomic region revealed by analysis of Bionano genomics data
BioRxIV 2017
Shao H et al
Rapid Automated Large Structural Variation Detection in a Diploid Genome by NanoChannel Based Next-Generation Mapping
BioRxIV 2017
Hastie A et al
De novo assembly and phasing of a Korean human genome
Nature 2016
Jeong-Sun Seo
Long-read sequencing and de novo assembly of a Chinese genome
Nature Communications 2016
Shi et al
Extensive sequencing of seven human genomes to characterize benchmark reference materials
Scientific Data (2016) 
Zook et al
Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays
Genetics 2016
Mak AC et al.,
Single Haplotype Assembly of the Human Genome from a Hydatidiform Mole.
Genome Research (2014); 24: 2066-2076 
Steinberg, K. et al.
Rapid Detection of Structural Variation in a Human Genome using Nanochannel-based Genome Mapping Technology.
Giga Science 2014
Cao, H., et al.
Finished Sequence and Assembly of the DUF1220-rich 1q21 Region Using a Haploid Human Genome.
BioMed Central Genomics (2014); 15(July 2014): 387 
O’Bleness, M., et al.
Genome mapping on Nanochannel arrays for structural variation analysis and sequence assembly.
Nature Biotechnology (2012); 30(8):771 
Lam, E.T., et al.

Videos

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Dr. Pui Kwok
University of California San Francisco, USA
Dr. Kwok discusses Bionano structural variant discovery in human diseases
Dr. Jaroslav Dolezel
Institute of Experimental Biology, Czech Republic
Dr. Jaroslav Dolezel discusses his work in plant genetics
Dr. Josh Udall
Brigham Young University,
USA
Dr. Udall discusses Bionano mapping and the cotton genome
Dr. Sue Brown
Kansas State University,
USA
Dr. Brown shares how Bionano genome maps help validate assemblies
Dr. Vanessa Hayes
Garvan Institute for Medical Research, Australia
Dr. Hayes discusses how Bionano aids her work prostate cancer

Webinars

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Bionano Saphyr Access
Bionano Access 1.1 and Bionano Solve 3.1 – Overview
Bionano Genomics
View Webinar Recording (May require download of GoToMeeting player)
Next Generation Karyotyping: Detecting Cancer-Associated Structural Variants Using Bionano Optical Maps.
Penn State Hershey
Dr. James Broach
View Webinar Recording (May require download of GoToMeeting player)
Download Webinar Presentation
Bionano Access for Saphyr Genome Mapping
Bionano Access 1.0 and Bionano Solve 3.0 – Overview
Bionano Genomics
View Webinar Recording (May require download of GoToMeeting player)
Vanessa Hayes
Bionano Webinar Series – Applications of Bionano Next-generation Mapping (NGM) Method to Cancer Patients – NGS is not Enough
Garvan Institute of Medical Research
Dr. Vanessa Hayes, PhD
View Webinar Recording (May require download of GoToMeeting player)
Eric Vilain
Bionano Webinar Series – Bionano Structural Variation Detection Helps Resolve Undiagnosed Genetic Disorders
Chief of Medical Genetics at UCLA
Dr. Eric Vilain, MD, PhD
View Webinar Recording (May require download of GoToMeeting player)
Alex Harkess
Bionano Optical Maps Help Solving Mystery of Garden Asparagus Sex Chromosomes.
Donald Danforth Plant Science Center
Alex Harkess
View Webinar Recording (May require download of GoToMeeting player)
Florian Jupe
Structural Variation Analysis within the Arabidopsis 1,001 Epigenomes Project
Salk Institute of Biological Studies
Florian Jupe
View Webinar Recording (May require download of GoToMeeting player)
gEVAL- A Genome Evaluation Browser for Improving Genome Assemblies
Wellcome Trust Sanger Institute
William Chow
View Webinar Recording (May require download of GoToMeeting player)
Using BioNano Maps to Improve an Insect Genome Assembly​
Kansas State University
Dr. Sue Brown
View Webinar Recording (May require download of GoToMeeting player)
Bridging the Gap between Micro and Macro: Genetic and Structural Variation in the Tomato Clade
Wageningen University
Dr. Gabino Sanchez Perez
View Webinar Recording (May require download of GoToMeeting player)
Diploid Genomic Architecture of an Individual Human
Icahn School of Medicine at Mount Sinai
Dr. Ali Bashir and Dr. Bobby Sebra
View Webinar Recording (May require download of GoToMeeting player)
Using Genome Maps to Create Accurate Human Genome Assemblies
The Genome Institute at Washington University
Tina Graves
View Webinar Recording (May require download of GoToMeeting player)
Mapping Single Chromosomes of Polyploid Wheat Using NanoChannel Arrays
Institute of Experimental Botany, Olomouc
Dr. Jaroslav Dolezel
View Webinar Recording (May require download of GoToMeeting player)
Toward Rapid Validation of Coding Fusions in Cancer Genomes: Multiple Myeloma First
Emory University
Dr. Michael Rossi
View Webinar Recording (May require download of GoToMeeting player)

Posters

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A Novel Method for Isolating High-Quality UHMW DNA from 10 mg of Freshly Frozen or Liquid-Preserved Animal and Human Tissue Including Solid Tumors
April, 2019
AACR, Atlanta, GA
Comprehensive Structural Analysis of Cancer Genomes by Genome Mapping​
April, 2019
AACR, Atlanta, GA
Comprehensive Detection of Germline and Somatic Structural Mutation in Cancer Genomes by Bionano Genomics Optical Mapping​
April, 2019
AACR, Atlanta, GA
Bionano Hybrid Scaffold Assemblies Provide High Contiguity and Accuracy
January 2019
PAG, San Diego, CA
Solution-based Isolation of Ultra-High Molecular Weight Genomic DNA from 0.2-0.5 mL of Frozen Human Blood (1.5 million WBCs) in less than 3 Hours
October 2018
ASHG, San Diego, CA
Hybrid Scaffolding with Bionano Genomics DLS Assemblies Provides High Contiguity and Corrects Errors in Sequence Assemblies
October 2018
ASHG, San Diego, CA
Sensitive Detection of Low-allele Fraction Structural Variants in Clinical Cancer Samples
October 2018
ASHG, San Diego, CA
Comprehensive Detection of Germline and Somatic Structural Mutation in Cancer Genomes by Bionano Genomics Optical Mapping
October 2018
ASHG, San Diego, CA
Building High Quality, Chromosome-Scale, De Novo Genome Assemblies by Scaffolding Next-Generation Sequencing Assemblies with Bionano Genome Maps
February, 2018
Advances in Genome Technology and Biology, Orlando, Fl
Broad Range Chromosomal Abnormality Detection through Bionano Genome Mapping
February, 2018
Advances in Genome Biology and Technology, Orlando, Fl
Labeling Human DNA with Bionano’s Direct Labeling Enzyme Avoids Nickase-Based Double-Stranded Breaks and Allows for Chromosome-Arm Length Assemblies
February, 2018
Advances in Genome Biology and Technology, Orlando, Fl
Efficient Structural Variation Detection and Annotation Using Bionano Genome Mapping
February, 2018
Advances in Genome Biology and Technology, Orlando, Fl
Efficient Structural Variation Analysis and Annotation using Bionano’s Next-Generation Mapping (NGM)
May, 2017
European Society of Human Genetics Annual Meeting, Copenhagen, Denmark
Next-Generation Mapping: Application to Clinically Relevant Structural Variation Analysis
May, 2017
European Society of Human Genetics Annual Meeting, Copenhagen, Denmark
Use of Bionano Optical Maps to Identify Medically-Relevant Genomic Variation
March, 2017
ACMG Annual Clinical Genetics Meeting, Phoenix, Arizona
Detecting a Novel Range of Large Somatic Genomic Rearrangements in Human Cancer Using the Bionano Optical Mapper
February, 2017
Advances in Genome Biology and Technology 2017 General Meeting, Hollywood, FL
Potential for improved molecular diagnosis of facioscapulohumeral dystrophy (FSHD) through D4Z4 array quantitation using Bionano Optical Maps
February, 2017
Advances in Genome Biology and Technology 2017 General Meeting, Hollywood, FL
Structural Variation Landscape Across 26 Human Populations Reveals Population Specific Variation Patterns in Complex Genomic regions
February, 2017
Advances in Genome Biology and Technology 2017 General Meeting, Hollywood, FL
Genome-Wide, Highly Sensitive and Accurate Structural Variation Detection in Plants and Animals by Next-Generation Mapping
January, 2017
Plant and Animal Genome Conference XXV, San Diego, CA
The Versatility of Next-Generation Mapping: An Encyclopedia of Genomes
January, 2017
Plant and Animal Genome Conference XXV, San Diego, CA
Accessing the Genomic Dark Matter: Using Next-Generation Mapping to Identify Large-Scale Repeat Structures in Maize
January, 2107
Plant and Animal Genome Conference XXV, San Diego, CA
Building High-quality, de novo Genome Assemblies by Scaffolding Next-Generation Sequencing with BioNano’s Next-Generation Mapping
January, 2017
Plant and Animal Genome Conference XXV, San Diego, CA
High Molecular Weight DNA Isolation from Plant Tissue for Next-Generation Mapping Applications
January, 2017
Plant and Animal Genome Conference XXV, San Diego, CA
In Silico and Biological Validation of BioNano Mapping Based Insertion, Deletion and Translocation Detection
October, 2016
American Society of Human Genetics, Vancouver, Canada
Next-Generation Mapping: A Highly Sensitive and Accurate Method for Interrogation of Clinically Relevant Structural Variation
October, 2016
American Society of Human Genetics, Vancouver, Canada
NanoChannel Array Based Genome Mapping Reveals “Dark Matter” in the Genome: Enabling Comprehensive Genome Wide Large Structural Variation Analysis in Population Studies
October, 2016
American Society of Human Genetics, Vancouver, Canada
Irys Next-Generation Mapping to Identify Medically-Relevant Genomic Structural Variation
October, 2016
American Society of Human Genetics, San Diego, CA
Clinically Relevant Structural Variations
March, 2016
Annual Clinical Genetics Meeting, Tampa, FL
De Novo Assembly and SV Detection of Human Genomes
February, 2016
Advances in Genome Biology and Technology, Orlando, FL
Complex Structural Variations and True Contiguity of de novo Assembly
February, 2016
Advances in Genome Biology and Technology, Orlando, FL
High-quality Assemblies
January, 2016
Plant and Animal Genome Conference XVII, San Diego, CA
Hummingbird Genome
January, 2016
Plant and Animal Genome Conference XVII, San Diego, CA
Fragile Site Repair
January, 2016
Plant and Animal Genome Conference XVII, San Diego, CA
rDNA Copy Number Variation
January, 2016
Plant and Animal Genome Conference XVII, San Diego, CA
Ultra-HMW DNA
January, 2016
Plant and Animal Genome Conference XVII, San Diego, CA
Structural variations, de novo assembly
October, 2015
American Society of Human Genetics, Baltimore, MD
Resizing N-Base Gaps
October, 2015
American Society of Human Genetics, Baltimore, MD
Analysis of HCC1143, inter-chromosomal translocation cells, CNV profiling
October, 2015
American Society of Human Genetics, Baltimore, MD
Amylase structural variants, Ashkenazi trio, SV calls
October, 2015
American Society of Human Genetics, Baltimore, MD
Hybrid scaffold, genome map assembly and complex insertions
October, 2015
American Society of Human Genetics, Baltimore, MD
Amylase variants, Ashkenazi trio and DNA absent from references.
May 2015 / June 2015
Biology of Genomes / European Society of Human Genetics, Cold Spring Harbor, NY (USA) / Glasgow (UK)
Copy-number profiles, translocation events and phasing.
May 2015 / June 2015
Biology of Genomes / European Society of Human Genetics, Cold Spring Harbor, NY (USA) / Glasgow (UK)
Pipeline overviews, hybrid scaffolds and complex insertions.
May 2015 / June 2015
Biology of Genomes / European Society of Human Genetics, Cold Spring Harbor, NY (USA) / Glasgow (UK)
CEPH Trio, multiple myeloma and prostate cancer.
April 2015 / June 2015
American Association for Cancer Research / European Society of Human Genetics, Philadelphia, PA (USA) / Glasgow (UK)
A closer look at how NanoChannel Arrays work and the effect they have on cancer genomes.
February, 2015
Biophysical Society, Baltimore, MD
Repeats in plant and animal genomes, SV calls in diploids, copy number variation and hybrid scaffolding.
February, 2015
Advances in Genome Biology and Technology, Marco Island, FL
Multiplexing, triplex forming oligo and epigenetic-state detection.
February, 2015
Advances in Genome Biology and Technology, Marco Island, FL
Integration events (YH genome), inheritance patterns (trio), breast cancer and CNV in tRNA.
February, 2015
Advances in Genome Biology and Technology, Marco Island, FL
De novo assembly of Chinese honey bee and Gandoerma Sinesis.
January, 2015
Plant and Animal Genome XXIII, San Diego, CA
Repeats in plants and animals, intact long tandem repeat arrays.
January, 2015
Plant and Animal Genome XXIII, San Diego, CA
Model parameters, copy number profiles, heterozygous deletion.
January, 2015
Plant and Animal Genome XXIII, San Diego, CA
SVs, CNV, unreferenced DNA, breast cancer.
November, 2014
Precision Medicine: Personal Genomes & Pharmacogenomics, Cold Spring Harbor, NY
De novo assemblies and structural variations in cancer genomes.
October, 2014
Beyond the Genome, Boston, MA
Hybrid scaffolding and assemblies of various genomes.
October, 2014
American Society of Human Genetics, San Diego, CA
Analysis of YH and trio samples.
October, 2014
American Society of Human Genetics, San Diego, CA
Long tandem repeats and copy number variation.
October, 2014
American Society of Human Genetics, San Diego, CA
De novo assemblies and structural variations in iPSC.
October, 2014
American Society of Human Genetics, San Diego, CA
Hybrid scaffolding, co-assembly and copy number profiles in cancer.
September, 2014
Human Genome Variation, Belfast, Ireland
Superscaffolding of Arabidopsis and de novo assembly of wheat (7DS).
September, 2014
Plant Genomics, St. Loius, MO
CNV validation, genome map assembly statistics and tandem repeats.
June, 2014
European Society of Human Genetics, Milan, Italy
Translocations, structural variation and CNV detection in multiple myeloma.
June, 2014
European Society of Human Genetics, Milan, Italy
Normalized copy number profiles, balanced translocations and complete genome characterization.
May, 2014
Sequencing, Finishing, Analysis in the Future, Santa Fe, NM
High throughput computing for de novo assembly.
May, 2014
Sequencing, Finishing, Analysis in the Future, Santa Fe, NM
Lp(A) repeat copy number diversity, multiple myeloma and MHC haplotype assembly.
May, 2014
Biology of Genomes, Cold Spring Harbor, NY
Structural variation discovery, MHC haplotype assembly, scaffolding de novo assembly and multiplexing.
February, 2014
Advances in Genome Biology and Technology, Marco Island, FL
De novo assembly of rice, Arabidopsis, wheat, and spider mite.
January, 2014
Plant and Animal Genome Conference XVII, San Diego, CA
Cancer structural variation, rearrangements, and pharmcogenomic variants in humans.
November, 2013
Precision Medicine: Personal Genomes & Pharmacogenomics, Cold Spring Harbor, NY
Human de novo assembly, multiple myeloma balanced translocation, genome-wide structural variation, and viral insertion localization.
October, 2013
American Society of Human Genetics, Boston, MA
Human structural variation detection, spanning gaps in hg19, scaffolding third gen sequencing, genome-wide SV detection, amplifications and expansions, and phasing of MHC variation.
June, 2013
European Society of Human Genetics, Paris, France
Assembly of variable rearranged regions in human (IGH and KIR), and Tribolium de novo genome scaffolding.
May, 2013
Sequencing, Finishing, Analysis in the Future, Santa Fe, NM
Human de novo assembly, genome-wide structural variation detection, super-scaffolding spider mite, scaffolding third gen sequencing, and wheat assembly using two-color data.
May, 2013
Biology of Genomes, Cold Spring Harbor, NY
Structural variation in humans, elucidating repetitive regions in yeast, and scaffolding broken genes in spider mite.
February, 2013
Advances in Genome Biology and Technology, Marco Island, FL
De novo assemblies of S. pombe, spider mite, and wheat (two-color).
January, 2013
Plant and Animal Genome Conference XXI, San Diego, CA
De novo assembly, scaffolding, and structural variation analysis of Drosophila.
November, 2012
American Society of Human Genetics, San Francisco, CA

Literature

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white papers
Next-Generation Cytogenetics: Bionano Whole Genome Mapping Resolves Structural Variants in Heterogeneous Cancer Samples

Bionano optical genome mapping 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
Bionano Genome Mapping Identifies Large Structural Variants in Cancer and Genetic Disorders

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 Mapping is able to detect all SV types with high sensitivity and specificity, and examples of cancer and genetic disease are shown.

white papers
Hybrid Scaffolding Improves Genome Assembly Accuracy and Contiguity

This white paper explains how Bionano NGM can make any sequency 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.

white papers
Bionano Genomics’ Next-Generation Mapping Identifies Large Structural Variants in Plant and Animal Genomes

This White Paper explains how NGS fails to adequately analyze repetitive parts of the genome and large structural variation. Bionano’s Next-Generation Mapping is able to detect all SV types with high sensitivity and specificity, and examples of biologically important large structural variants in plant and animal genomes are shown.

case studies
Assembling High Quality Human Genomes: Going Beyond the ‘$1,000 genome’

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
First Comprehensive View of Maize Genome Reveals Regulatory and Structural Mechanisms

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
Next-generation Mapping Enables Ideal Genome Assembly for Greater Duckweed

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.

Datasets

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