Better genetic mapping for better outcomes

WASHINGTON, D.C. & LOS ANGELES—A team of researchers from Children’s National Health System and the University of California, Los Angeles (UCLA) led by Dr. Eric Vilain have utilized Bionano Genomics’ Irys and Saphyr systems to identify pathogenic structural variants indicative of genetic diseases. Testing the systems on patients with Duchenne muscular dystrophy (DMD), they found that the mapping allowed by using Bionano technology presented a faster, more cost-effective and more accurate diagnosis than existing methods.

Bionano’s Irys and Saphyr systems are whole-genome analysis tools, designed to better understand and map genomic structures. Saphyr is an optical mapping solution that provides rapid, high-throughput, long-range genome mapping capable of detecting structural variations with extreme sensitivity, while Irys offers whole-genome maps at single-molecule resolution. In the UCLA study, Vilain’s team used both systems to identify pathogenic structural variants in a series of patients diagnosed with DMD, which is caused by large deletions, insertions and inversions disrupting the X-linked dystrophin gene. DMD is a severe degenerative muscle disorder mostly affecting boys, for which there is currently no cure.

Vilain showed that a single Bionano test can at times replace or outperform as many as four different tests. This work also illustrates how Bionano provides translational researchers with a tool that sees genome variations that other technologies miss. For example, one study subject had large structural variants that interfered with proper functioning of the X-linked dystrophin gene. He had been diagnosed with DMD through an invasive muscle biopsy, after chromosomal microarray, MLPA, PCR sequencing of all 79 exons and exome sequencing all failed to detect the pathogenic inversion.

Dr. Erik Holmlin, CEO of Bionano Genomics, comments, “We are excited by Dr. Vilain’s team demonstrating Bionano’s ability to correctly identify structural variants in patients with genetic disease. The current diagnostic process proves to be a true odyssey for many of the children and parents hoping to find answers or treatment. Dr. Vilain shows that in some cases a single Bionano test could replace or outperform up to four different tests, which would not only simplify testing, but would also dramatically shorten the search for answers. We are also happy with the illustration in this work of how Bionano provides translational researchers with a tool that sees genome variations that other technologies miss. We can’t wait to see how other scientists and physicians, inspired by these incredible results, use Bionano mapping in their genome studies and analyses.”

The study authors state in the publication that Bionano mapping “has the capacity to replace both MLPA and chromosomal microarrays in the clinical setting.” MLPA is a probe-based assay to detect the deletion or duplication of specific loci in the genome. For this study, the authors cite as key advantages over MLPA the ability of Bionano technology to provide order and orientation of structural variants and the ability to detect these variants genome-wide.

Comparing the tech to chromosomal microarray, Vilain’s team discussed Bionano’s capability to detect balanced events such as inversions and balanced translocations, as well as much smaller variations completely missed by microarray. Relative to next-generation sequencing, the authors stated that Bionano provides higher sensitivity for large structural variants with better false-positive and false-negative rates. Turnaround time and cost are comparable to the aforementioned tests. The study concludes that Bionano mapping “is poised to become a new tool in the clinical genetic diagnostic strategy and research due to its ability to sensitively identify large genomic variations.”

According to Holmlin, more than half of patients with genetic diseases fail to get definitive molecular diagnoses. “While it is clinically evident that there is a pathology, doctors are often unable to pinpoint a precise diagnosis,” he says. “Our research will help close that gap.”

According to Holmlin, Vilain’s discovery suggests more uses for the Irys and Saphyr systems will follow. They have already been tested on hematological malignancies, and translational research is underway in prostate cancer studies as well. Because cancer is a disease of structural variations, says Holmlin, the technologies should be effective in solid tumors, as well as other oncological practices. While the mapping capacity may not lead directly to a cure, its efficacy and specificity can be utilized to guide trials that aim to restore proper function when molecular variations are present. As more early adopters stretch the capacity of the Bionano systems, new reagents, software applications, assays and other products will be added to pipeline.