Saphyr System to Aid GeneDx in Detecting Mutations Causing Various Muscular Dystrophies

Joana Carvalho, PhD avatar

by Joana Carvalho, PhD |

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GeneDx has chosen Bionano Genomics’ technology, called Saphyr System, to aid in developing tests to detect mutations in genes that are associated with different forms of muscular dystrophy and other disorders.

Saphyr is a whole-genome imaging technology that uses advanced optics combined with mathematical algorithms and machine learning to identify alterations throughout the genome (all genes found in DNA). According to Bionano, the algorithms that Saphyr is based on allow it to give results with greater sensitivity than other gene sequencing-based technologies, meaning fewer false positives.

Another, previously suggested advantage of Saphyr to techniques such as next generation sequencing (NGS) is that it is able to detect large genetic alterations anywhere in the genome. These include, for instance, repeat contractions often seen in individuals with facioscapulohumeral muscular dystrophy (FSHD), and repeat expansions associated with myotonic dystrophy.

Such genetic alterations consist in the loss (contractions) or addition (expansions) of repetitive portions of the DNA sequence.

“Saphyr addresses the need for more and better patient testing for diagnosis and research in drug development. GeneDx’s adoption of the Saphyr System illustrates the need for advanced tools to test for conditions caused by large structural variants [mutations] where short-range NGS isn’t ideal,” Erik Holmlin, PhD, CEO of Bionano, said in a press release.

“We are excited that the Bionano technology will enable GeneDx to bring a new generation of assays to the clinic,” Holmlin added.

Saphyr complements Gene Dx’s current core technologies, Bionano said. The technology, to be used in Gene Dx’s clinical laboratory in Gaithersburg, Maryland, is expected to accelerate the development of new assays, or tests, that will facilitate the identification of mutations linked to muscular dystrophies, and developmental and reproductive disorders.

“GeneDx was one of the first commercial laboratories to offer Sanger sequencing for monogenic [single gene] disorders and multigene panels and implement microarray for copy number events, as well as [NGS] panels and to introduce exome sequencing,” Sean Hofherr, PhD, chief scientific officer at GeneDx, said.

Copy number events are variations in the number of copies of a particular gene among individuals. The exome refers to all the DNA bits with information to generate proteins (exons).

“We are proud to continue our history of being a clinical genomics pioneer, and be one of the first commercial laboratories to develop and validate assays based on the Bionano Saphyr System in a clinical setting under CLIA/CAP guidelines,” Hofherr added. “The Saphyr technology is groundbreaking and will allow us to look at the ‘dark matter of the genome.’”

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