Direct Label and Stain Technology

Innovation That Makes Everything Better

Prior to DLS, DNA was labeled using nicking endonucleases to make sequence-specific nicks, which are fluorescently labeled and then repaired. This process is highly robust and specific, but when nick sites are close together on opposite strands it introduces systematic double-stranded breaks that limit the contiguity of Bionano maps.

The DLS chemistry leaves sample DNA intact, eliminating systematic molecule breaks. The DLS protocol consists of a single enzymatic labeling reaction, followed by cleaning and staining. There is no need to repair nicks, which makes for a more streamlined protocol.

DLS delivers the best possible genome mapping at a fraction of the cost.

• Longest molecules ever achieved – DLS-labeled molecules can be substantially longer with > 2 Mbp native molecules seen often.
• Chromosome arm-length maps ­– DLS genome maps are 50-fold longer on average, improving visualization of genome structure and creating the most contiguous and accurate assemblies. Chromosome arms and full chromosomes are often assembled in single maps.

Maps built from nickase-based labeling methods (NLRS, top) cover the entire human chromosome 3 for comprehensive SV detection, but are highly fragmented. With DLS (bottom), each chromosome arm is covered in just one map for each haplotype.

Maps built from nickase-based labeling methods (NLRS, top) cover the entire human chromosome 3 for comprehensive SV detection, but are highly fragmented. With DLS (bottom), each chromosome arm is covered in just one map for each haplotype.

Maps built from nickase-based labeling methods (NLRS, top) cover the entire human chromosome 3 for comprehensive SV detection, but are highly fragmented. With DLS (bottom), each chromosome arm is covered in just one map for each haplotype.

• Structural variation detection starting at 500 bp – DLS improves sensitivity for all structural variants with insertions and deletions detected at 500 bp.
• $500 per (human, or human-size) genome total cost – DLS makes high-volume mapping more affordable and attainable for Bionano users.

DLS sample prep kits are available now for Saphyr™ users. Order DLS Prep Kits

DLS for Structural Variation Detection

DLS further improves Bionano’s industry-leading structural variation detection and ability to elucidate complex rearrangements. With single maps per haplotype per chromosome arm, complex rearrangements are visualized in a single contiguous map.

DLS assembles the entire human chromosome 10 in two single maps, separated by the centromere (top). Gene positions are shown in green. Insert shows multiple large rearrangements assembled into a single map in the 10q11.21 region involved in intellectual disability/developmental delay.

DLS assembles the entire human chromosome 10 in two single maps, separated by the centromere (top). Gene positions are shown in green. Insert shows multiple large rearrangements assembled into a single map in the 10q11.21 region involved in intellectual disability/developmental delay.

DLS assembles the entire human chromosome 10 in two single maps, separated by the centromere (top). Gene positions are shown in green. Insert shows multiple large rearrangements assembled into a single map in the 10q11.21 region involved in intellectual disability/developmental delay.

Chromosome arm-length maps mean that there is no upper limit to the variants detected. DLS greatly enhances your ability to detect multi-megabase-pair events at high sensitivity. Plus, a new per-label copy number analysis algorithm normalizes the raw coverage profile to provide copy number calls for detection of aneuploidy, loss of chromosome arms, and large insertions and deletions above 500 kbp.

Two varieties of sunflower are mapped with DLS and de novo assembled into extremely long maps. Large structural variants between the two varieties are identified.

Two varieties of sunflower are mapped with DLS and de novo assembled into extremely long maps. Large structural variants between the two varieties are identified.

Two varieties of sunflower are mapped with DLS and de novo assembled into extremely long maps. Large structural variants between the two varieties are identified.

Chromosome arm-length maps and new copy number (CN) profiling provide a robust tool for large scale SV detection and visualization, here showing a 27 Mbp deletion found in the genome of a leukemia patient. The same deletion is detected independently from the consensus genome map as well (blue map aligned to reference in green). Molecules aligning to the genome map are shown below.

Chromosome arm-length maps and new copy number (CN) profiling provide a robust tool for large scale SV detection and visualization, here showing a 27 Mbp deletion found in the genome of a leukemia patient. The same deletion is detected independently from the consensus genome map as well (blue map aligned to reference in green). Molecules aligning to the genome map are shown below.

Chromosome arm-length maps and new copy number (CN) profiling provide a robust tool for large scale SV detection and visualization, here showing a 27 Mbp deletion found in the genome of a leukemia patient. The same deletion is detected independently from the consensus genome map as well (blue map aligned to reference in green). Molecules aligning to the genome map are shown below.

Enhanced sensitivity for all variants starting at 500 bp

Bionano algorithms call all major structural variants (SV) with sensitivities up to 99% and PPV over 98%. SV detection with a single DLS assembly is as sensitive or better than detection using data from two nickase assemblies. DLS detects translocations starting at 50 kbp, and large insertions with higher sensitivity than previous methods.

DLE-1, the first enzyme in the DLS family, has an increased label density in a human genome, which achieves detection of insertions and deletions starting at 500 bp. This size range represents a significant improvement over the 1,000 bp lower limit of nickase-based methods. Compared to the insertions and deletions NGS detects in a human genome, Bionano SV calls differ by a median of only 60 bp.

Double the output. Fraction of the cost.

DLS reduces the cost per (human, or human-size) genome down to $500 for high-throughput users. Previously, achieving the highest SV sensitivity required mapping a genome with two separate nick labeling reactions. Now, only a single DLS reaction is required.

With DLS, you effectively double the throughput of Saphyr for SV detection, enabling the mapping of two human genomes per Saphyr Chip in one 24-hour run.

DLS for Genome Assembly

Bionano de novo genome assemblies yield the best contiguity ever seen. The contiguity of maps generated with DLS takes Bionano genome assembly quality to an even higher level. In addition, the DLE-1 enzyme is compatible with a wide variety of organisms, enabling rapid, high-quality genome assembly in virtually all areas of research.

Organisms de novo assembled using Bionano direct labeling chemistry (DLS). De novo assemblies often cover whole chromosome arms, only broken at centromeres and other low complexity regions which are longer than the largest mapped molecules.

Organisms de novo assembled using Bionano direct labeling chemistry (DLS). De novo assemblies often cover whole chromosome arms, only broken at centromeres and other low complexity regions which are longer than the largest mapped molecules.

Organisms de novo assembled using Bionano direct labeling chemistry (DLS). De novo assemblies often cover whole chromosome arms, only broken at centromeres and other low complexity regions which are longer than the largest mapped molecules.

Contiguity up to chromosome lengths

De novo assemblies from DLS-labeled genomes are some of the most contiguous possible, typically offering full chromosome arm scaffolds. We have also achieved full chromosome scaffolds in certain plant and animal genomes.

Assemblies created with DLS set the bar for contiguity and scaffold accuracy, often exceeding recent reference genome publications.

Maize sequence assembly scaffolded with DLS is 10 times more contiguous than the maize reference genome recently published in Nature (546), 524–527 (22 June 2017).

Maize sequence assembly scaffolded with DLS is 10 times more contiguous than the maize reference genome recently published in Nature (546), 524–527 (22 June 2017).

Maize sequence assembly scaffolded with DLS is 10 times more contiguous than the maize reference genome recently published in Nature (546), 524–527 (22 June 2017).

Make the most of sequencing data

With chromosome arm lengths, Bionano maps form an entirely independent map of the genome, which is used to validate and correct sequence contigs. Chimeric sequence contigs, a common source of sequence assembly errors, are cut automatically.

DLS is compatible with all NGS sequencing data. A high-quality NGS sequence assembled with DLS maps yields better results. For less contiguous NGS assemblies, DLS can be combined with Bionano NLRS labeling to incorporate more of the sequence into the assembly, thereby lowering sequencing costs and improving results.

DLS technical requirements

DLS is compatible with DNA isolated by any Bionano Prep protocol.

Bionano Access™ v1.2 and Bionano Solve v3.2 are optimized to work with DLS, with typical human de novo assemblies taking less than 30 hours on a single Saphyr or Bionano Compute.

DLS is not compatible with Irys^® systems. Contact us for an upgrade offer if you are interested in upgrading from Irys to Saphyr.