Why are genomic maps important?
BioNano Genomics specializes in creating instruments that aid in the construction of powerful physical genomic maps. A physical map gives information about the order of genes, single nucleotide polymorphisms (SNPs), and other genetic features, as well as the distance between these regions and markers. This information is invaluable in understanding the relationships between gene regions. It can also detect structural changes in the genome, such as indels and genetic rearrangements.
Traditional methods of variant detection, such as fosmid end sequencing and paired end mapping, could detect indels (insertions and deletions) of 1 kb or greater. With optical mapping, however, indels of 50 bp lengths can be detected with high confidence. This accuracy allows for correction to be made in reference genomes with regard to repeat regions, indels, and other structural variants.
Next-generation sequencing technologies often break DNA up into smaller, more manageable pieces before working with them. While this technique has allowed for increased sequencing speed, it has also sacrificed the ability to see long-range connectivity of genes. In areas where the genetic information is repeated, this is especially dangerous and can lead to error in sequencing results. BioNano technology uses high-molecular weight DNA (>100 kb) to overcome this difficulty and ensure accuracy regarding physical distances between genetic markers.
(1) Isolate high-molecular weight DNA. In plant genomes, such as cotton, this can prove difficult. Many naturally occurring chemicals get in the way of DNA isolation, such a polyphenols. To isolate the long strands of DNA, a detailed process is used to gently purify DNA, while maintaining its length.
(2) Label the DNA. Enzymes that recognize specific sequences are used to "nick", or break a single strand of DNA at certain points. The DNA is then labelled with a fluorescent tag at sites where it was nicked.
(3) Load the Irys machine. Labelled DNA is loaded into an Irys chip and placed in the machine. A current is applied to the chip, which forces the DNA through nano-channels that linearize the DNA.
(4) Image the labelled DNA. As DNA passes through Irys chip nano-channels, a high-resolution camera produces images of the DNA backbone and the fluorescent sites.
Advantages of Optical Mapping Technology
-Novel insertions and deletions are found with high accuracy
-No insertions bias. Deletions can be detected just as easily as insertions.
-Copy number correction
Disadvantages of Optical Mapping Technology
-Dependence on a reference genome
-Restriction enzyme efficiency
-Limited public knowledge of technology
Optical mapping using the Irys platform is a method to detect structural variation. It is being used to create more robust reference genomes, as well as detect structural variants in genome evolution. Optical mapping ought not to be considered the only way to detect structural variation, but rather another technique in the arsenal of variant detection. When compared to traditional methods, however, optical mapping excels in characterizing
Achievements of Optical Mapping
-Identification of 4,000 new structural variants in the Human Genome
-Characterization of a large scale deletion associated with neurocognitive disease in humans
-Confirmation of rice genomic structure
-Clarification of highly variable regions in the human genome, such as the histocompatability complex