Long-range genomic information via optical maps

Bionano Genome Maps

Platform Overview

Optical genome maps are constructed basing on specific cutting sites of restriction enzymes along a single DNA molecule, which are unique DNA fingerprints. Therefore, these optical genome maps provide macro view of a DNA molecule structure and facilitate complete genome assembly. New labeling technology announced by BioNano, Direct label and stain (DLS), is applied to avoid destruction of chemistry during sequence motif labeling of genome DNA, which largely eliminates the affects of fragile sites on genome assembly. Compared to NLRS labeling technology, DLS could generate much longer optical map reads.



Genome Imaging Instrument

BioNano Irys is the first generation optical mapping analysis platform. Combining restriction enzyme cutting to fluorescent labeling on single DNA molecule, Irys generates high-resolution images of linear DNA structures. Since no PCR amplification is involved, systematic errors are largely avoid to reveal a more reliable structure of DNA. The system is compatible for sequence data from first, second and third generation sequencing.
BioNano Irys

BioNano Saphyr is the second generation optical mapping analysis platform. Saphyr employs the same technology as Irys, on top of which, Saphyr largely increases its throughput to achieve a faster detection and analysis of genome optical maps. In addition, Saphry provide data processing strategy and process data analysis automatically. It is a more efficient and cost-effective platform of next-generation mapping (NGM),
BioNano Saphyr

Saphyr Chip

Experimental Workflow



Key Advantages

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High accuracy
Optical mapping is constructed on base of non-damage DNA molecules without any amplification and fragmentation steps. Therefore, it represents the closest status to real DNA.
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Extremely Long reads
Optical mapping can achieve read length of hundreds of Kb or Mb. The longest N50 can reach 100+ Mbp, which could cover the repetitive regions. Therefore, it empowers us to overcome the difficulties of repetitive sequences in genome assembly.
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Determination of genome GAP
Optical mapping based genome assembly is based on the fixed sites of restricted enzyme cutting. Therefore, the gap between DNA fragments can be determined.
High completeness
High completeness
Up to 88-99% of NGS contigs is covered in hybrid scaffold. It is applicable to various species.
High-resolution fluorescent image of linear DNA molecule

A 2.34 Mbp molecule aligning to human chromosome 3 (Sadowski H B et al.,Bionano Genomics. 2018)

Organisms de novo assembled using DLS (Hastie A et al.,Bionano Genomics. 2018)

Comparable SV size between Bionano SV calls and PacBio (Hastie A et al.,Bionano Genomics. 2018)

Applications

Genome assembly

Saphyr chip contains 120,000 nano channels and real-time images of DNA molecules in these nano channels are acquired by high-resolution CCD camera. Up to 5 T data can be collected per flowcell. The assembled whole genome optical maps are constructed by automatic transferring of images to molecule data.

(1)Genome assembly correction

The contigs generated by Nanopore and PacBio can be ordered and anchored to chromosome by optical genome maps. In addition, these optical maps enables detection and correction of potential errors in genome assembly. Hi-C based alignment of contigs to chromosome-level scaffold may also contain errors in contig order and orientation, which can be corrected by Bionano optical maps.
7 misassembled contigs from PacBio (orange) were identified by Bionano alignment in maize genome (Liu J et al., Genome Biology.2020)

Mis-positioning of fragments by Hi-C were identified by Bionano optical mapping (Andy Wing et al.,Bionano Genomics. 2018)






(2)Improvements in scaffold

With assembled genome, thousands of contigs can be further assembled into several super-scaffolds by hybrid assembly with optical genome mapping, which largely enhanced the contiguity and quality of genome assembly.
Hybrid-scaffolding NGS sequence assembly with Bionano maps (Liu J et al., Genome Biology.2020)

Structural variation detection
Basing on single molecule fluorescent labeling, Bionano optical mapping can resolve large-scale structural variations, including Insertions/deletions, translocations, inversions, duplications. etc. Compared to previous tools, such as FISH, etc., Saphyr is superior in its high resolution, high genome coverage, user-friendly workflow and clear presentation of outcomes. The sensitivity of detection on variations with size of 500 bp to Mb is much better than sequencing platforms.
Detection sensitivity of structural variations by Bionano

Detection of SVs by optical maps (blue) and reference sequences(green) (Wang J et al., Bionano Genomics. 2018)

Successful Cases