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Next-generation mapping for genomic assemblies
July 2016
by Jeff Bouley/Rachel Flehinger  |  Email the author


SAN DIEGO—BioNano Genomics, which sees itself as the leader in physical genome mapping, announced recently the publication of another study describing application of its next-generation mapping (NGM) technology “as the critical component in achieving high-quality de-novo human genome assemblies with unprecedented contiguity.”
In the current study—titled “A hybrid approach for de novo human genome sequence assembly and phasing” and appearing in the May 2016 issue of Nature Methods—researchers combined NGM with Illumina-based approaches for next-generation sequencing (NGS) and demonstrated that when the GemCode Technology from 10X Genomics is used for sequencing library preparation, BioNano says, the resulting hybrid assembly has “comparable or slightly better contiguity to that of NGM-NGS hybrid assemblies achieved with PacBio in previous studies such as that which Pendleton and colleagues at Mt. Sinai published in a June 2015 issue of Nature Methods.”
“I’m pleased to see the growing use of NGM as a key tool in obtaining such high quality genome assemblies. The 10X approach makes it easier to integrate Illumina’s NGS together with NGM and expands the opportunity to create much better reference genomes,” said Dr. Erik Holmlin, president and CEO of BioNano Genomics. “Improving reference genomes will help applications of BioNano’s NGM as a standalone tool for discovery of novel, clinically and biologically relevant structural variations (SVs) as well as make NGM a more efficient approach to detecting those SVs already known for their clinical and translational applications.”
As a BioNano media representative told DDNews, two key takeaway points from the published paper are that researchers now have a new method of generating more complete human genome assemblies of longer length with fewer gaps and that BioNano’s Irys next-gen mapping tool is enabling researchers to better study human diseases and better identify new targets for therapeutics.
“Genomic information derived from long-range technologies allows us to take discovery several steps beyond that based solely on single nucleotide polymorphisms,” said Dr. Pui-Yan Kwok, senior author of the May 2016 article and the Henry Bachrach Distinguished Professor at the University of California, San Francisco (UCSF). “Using BioNano’s next-generation mapping solution in combination with medium-length contiguity information provided by newer sequencing methods, any researcher can produce highly contiguous de-novo genome assembly of complex genomes. Our approach makes it possible to detect structural variations with base pair resolution across the genome in one set of experiments and open up the field for many new applications.”
Kwok and colleagues at UCSF’s Cardiovascular Research Institute/Institute for Human Genetics and researchers at the University of Cape Town’s Department of Molecular and Cell Biology used BioNano’s Irys system to build physical maps of the genome in which long-range information spanning complex regions such as repeats and other structural variations is intact.
They integrated the maps with sequence assemblies based on Illumina short-read sequencing and library preparation from 10X Genomics for linked-reads. This combination of NGM, linked-reads and Illumina-based sequencing, similar to the combination of PacBio sequencing and NGM, overcomes limitations of NGS alone.
BioNano Genomics’ Irys system uses NanoChannel arrays integrated within the IrysChip to image genomes at the single-molecule level with average single-molecule lengths of about 350,000 base pairs. The long-range genomic information obtained with the Irys System helps decipher large, complex DNA repeats, which are the primary cause of inaccurate and incomplete genome assembly.
The month after the publication of the Nature Methods article, BioNano Genomics announced the release of an update to its Irys Data Solutions to improve SV analysis in human samples. In this new version, the IrysSolve tool enables better understanding of and improves sensitivity to the diploid nature of human genomes, enabling insights into complex diseases, including Mendelian diseases such as sickle-cell anemia and cystic fibrosis.
“The new ability to call for insertions and deletions on human diploid samples will make the adoption of the Irys System much easier than before,” said Kwok. “Following up on the previous work that my group published in the January edition of the journal Genetics, I was very impressed to see how those findings, which took over six months to generate, can now be generated in a matter of a few hours. In addition, the new pipeline was able to detect four times more SVs that were not detected previously. Validation for those is ongoing and we will be sharing those findings shortly. I am also especially impressed by the ability of the software to identify heterozygous insertions and deletions with a sensitivity of over 80 percent. Typically, NGS barely identifies 40 to 50 percent of heterozygous insertions and deletions.”
Code: E071604



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