AGBT: BioNano Launches New Labeling Approach

AS AGBT opened, optical mapping company BioNano Genomics announced a new scheme for labeling genomic DNA inputs which substantially improves performance.  Sven Bocklandt from the company sat down with me yesterday to walk through the new Direct Labeling
BioNano's goal is to use optical mapping to detect structural variants and improve genome assemblies.  DNA molecules are labeled at specific short sequence motifs and then run into long nanochannels which hold the DNA straight.  DNA within nanochannels is then imaged to measure the distances between labeled sites.  De novo assembly of these labeling patterns reveals the genomic structure of the input DNA.

In the original system, labeling was achieved by nicking the DNA with nickases, mutant restriction enzymes which cut on only one strand.  The initial nick would then be "translated" along the DNA by limited synthesis with an 5'-exonuclease positive DNA polymerase and fluorescent nucleotides  This labeling scheme relies on very well-worn molecular biology principles -- nick translation was invented in the late 1970s.  The catch is that if recognition sites for a given nickase lie in close proximity on opposite strands, then this procedure will generate a double-strand break and an insurmountable gap in the map for that nickase.  BioNano compensated for this by having two different labeling kits with two different nickases, which would mostly complement each other.  But if both should happen to generate a double-strand break near each other, then combining the data would not help.

With Direct Label and Stain (DLS) chemistry, a proprietary enzyme labels the DNA at a short motif without any cleavage of the phosphodiester backbone.  The effect on mapping quality is dramatic, with often 100-fold longer scaffolds.  Indeed, in human many chromosomes now resolve to four scaffolds, two per chromosome arm.  Sven did stress that there is likely haplotype switching within the homologous scaffolds.  Still, this is a remarkable achievement.  With volume purchases, consumables to generate such as map can be as low as $500 a sample, with sample to map times of about a week. However, only one day of that time is instrument time, so it is possible to run a higher throughput pipeline -- one customer is generating six human genome maps per week on a single Saphyr instrument (list price: $300K).  With high quality DNA extractions from agarose block embedded cells, BioNano sees DNA molecules well in excess of one megabase in length.  

For structural variant discovery, BioNano says they can detect indels as small as 500 basepairs, which is about one pixel on their instrument, though they cannot localize such variants within a span of two labeled sites.  For inversions and translocations, they see 95% sensitivity for alterations of 40 kilobases or greater.

DLS is supported only on the newer Saphyr systems; the original Iris systems cannot use this chemistry.  BioNano plans to work with the customer base for the Iris to replace these systems.