Bionano Genomics announced at the American Society of Human Genetics (ASHG) annual meeting in Houston that PerkinElmer Genomics and the University of Iowa have both adopted use of Bionano’s Saphyr whole-genome imaging platform in their assay development labs, with PerkinElmer being the first to develop and validate an assay based on the Saphyr system in a clinical setting under CLIA/CAP guidelines.
The lead indication for assay development by both organizations it Facioscapulohumeral Muscular Dystrophy (FSHD), which affects approximately 1 in 10,000 individuals and is one of the most prevalent forms of muscular dystrophy.
Saphyr is Bionano’s third-generation optical mapping solution, designed to detect structural variations ranging from 500 bp to megabase pairs in length. Saphyr offers assembly and discovery algorithms at sensitivities as high as 99%, with false positive rates below 2%—far outperforming sequencing-based technologies in sensitivity, according to Bionano.
PerkinElmer Genomics is the first U.S. laboratory to develop and validate an assay based on Bionano’s Saphyr optical mapping technology in a clinical setting under CAP/CLIA guidelines, the companies said.
“We have always believed that Bionano’s unique ability to image long, intact DNA molecules could enable the Saphyr system users to develop assays in a clinical setting to modernize and streamline the practice of cytogenetics,” Bionano CEO Erik Holmlin, Ph.D., said in a statement.
The longtime challenge for diagnosing FSHD has been tallying an exact count of the repeat number. Until now, molecular diagnoses for FSHD have been generated using Southern Blot techniques, which are imprecise, labor intensive and involve radioactive labeling methods which are being phased out of laboratory use for safety reasons.
PerkinElmer Genomics said the assays it has developed with the University of Iowa using the Bionano EnFocus FSHD Analysis tool are designed to provide an exact repeat number for the pathogenic and non-pathogenic variants, give a high-resolution view of the repeat regions and have a high sensitivity to mosaicism. As a result, said PerkinElmer Genomics, their assay overcomes the challenges of FSHD diagnosis by being reproducible, safe, fast, and automated with minimal hands-on time.
“We are committed to helping patients and families that need genetic testing and are excited about the strong clinical utility of this assay for the molecular assessment of FSHD patients,” stated Madhuri Hegde, Ph.D., FACMG, Vice President and CSO of PerkinElmer Genomics.
Jamshid Arjomand, Ph.D., CSO of the FSHD Society, a patient organization focused on the disease, added that the lack of an accurate molecular diagnosis has limited successful recruitment into the growing number of clinical research studies and clinical trials for the disease.
“We are delighted that Bionano’s Saphyr system enables a more precise and higher throughput method for FSHD genetic testing and are grateful to diagnostic groups and companies that are making genetic testing more accessible to our families,” Arjomand said.
Bionano said it will make a recording of the presentation available on its website, and will also showcase the Bionano EnFocus FSHD Analysis tool for fast, streamlined bioinformatics assessment of the FSHD locus from genome-wide optical mapping data at booth #527.
“We believe Saphyr is ready to be adopted for assay development in a routine clinical workflow, and we are thrilled that PerkinElmer Genomics and the University of Iowa are taking the lead in making the Saphyr system a tool for next-generation cytogenomics, with many other academic, CRO and reference laboratories expected to follow,” Holmlin said. “We believe that FSHD is just the start of a wide array of clinical genetics assays that labs will develop with our technology.”