Bionano offers an end to end solution for analysis of structural variation. The workflow includes sample preparation, DNA imaging and genomic data analysis technologies combined into one streamlined workflow that enables you to identify structural variants and create de novo genome assemblies like never before.
Sample Preparation
Bionano sample preparation kits provide everything needed to isolate ultra-high molecular weight DNA from fresh or frozen blood, cultured cells, and plant and animal tissues.
Bionano’s sample prep method produces the large molecules, greater than 150 kbp, needed for assembly.
Bionano provides two methods to isolate ultra-high molecular weight DNA that is compatible with Saphyr: a solution-based method called Bionano Prep SP, and a method based on agarose gel plug DNA isolation.
This Bionano Prep SP Blood and Cell Culture DNA Isolation Kit can provide ultra-high molecular weight DNA in less than 4 hours for EDTA-collected blood and mammalian cell cultures. It utilizes a lyse, bind, wash, and elute procedure that is common for silica-based DNA extraction technologies in combination with a novel paramagnetic disk. Unlike magnetic beads and silica spin columns, which shear large DNA, the Nanobind Disk binds and releases DNA with significantly less fragmentation.
For ultra-high molecular weight DNA isolation from plant, animal and human tissues, detailed protocols are provided to users. These protocols are based on the isolation of cells or nuclei in an agarose matrix, where DNA purification takes place while the molecules are stabilized in agarose. By the end of the purification process, the agarose is digested and molecules up to chromosome arm lengths in size are released.
Sample Labelling
The Bionano DNA labelling kit provides the reagents needed to label DNA at specific sequence motifs for imaging and identification. These labelling steps result in a uniquely identifiable sequence-specific pattern of labels to be used for de novo map assembly.
The primary chemistry, Direct Label and Stain (DLS), recognizes a 6 base pair sequence motif and transfers a fluorescent label directly to it in a single enzymatic step.
Linearization and Imaging
A labeled DNA sample is pipetted onto the Saphyr Chip™ in one of the flowcells. Saphyr electrophoretically controls the movement of DNA in the flowcell. A gradient of micro- and nano-structures, upstream of Saphyr Chip’s NanoChannels, gently unwinds and guides DNA into the NanoChannels.
Saphyr Chip’s NanoChannels allow only a single linearized DNA molecule to travel through while preventing the molecule from tangling or folding back on itself. The nanofluidic environment allows molecules to move swiftly through hundreds of thousands of parallel NanoChannels simultaneously, enabling high-throughput processing to build an accurate Bionano genome map.
De Novo Genome Map Assembly
Once raw image data of labeled long DNA molecules is captured by the Saphyr instrument, it is converted into digital representations of the motif-specific label pattern. Bionano Solve™ data analysis software then assembles the data de novo to recreate a whole genome map assembly.
