Traditional next-generation sequencing (NGS) technology excels in detecting small variant mutations that can cause disease. However, the human genome also contains structural variants (SVs), which account for the largest number of divergent base pairs in the genome. Most cannot be detected by short-read sequencing technologies, which suffer from low sensitivity and high false positive rates. Bionano’s Saphyr combined with our new DLS labeling chemistry and a suite of analysis tools has much better sensitivity and true positive rates when calling structural variants of all types than sequencing based methods.
While Bionano’s SV calls are sufficient for many applications, some more complex indications require a tight integration with the smaller NGS-called variants. To make this integration possible, Bionano is now working with the global health company Genoox to develop a genome informatics workflow to integrate and annotate Bionano structural variant calls with sequencing data within the Genoox platform.
Genoox’ analysis pipeline already provides clinical annotation and analysis of the human genome, based on NGS data. By using Genoox technology for aligning short read sequence data to Bionano’s SV calls, the high sensitivity of Bionano calls should be combined with the basepair precision of NGS.
The Genoox integrated platform is designed to identify SV breakpoints to single base pair resolution if matching NGS reads are available; cross-validate the Bionano and NGS variant calls, thereby increasing the calling confidence; enable the detection of a comprehensive set of both SNV and SV mutations on one common platform; and utilize the Genoox platform for automatic processing, annotation, data integration and reporting of results.
The Center for Genetic Medicine Research at Children’s National Health System in Washington D.C. will be the initial user of the Genoox integrated platform. The new technology offers Children’s National a single platform for sensitive, accurate detection of structural variations and genetic mutations for rare disease, not previously possible, helping to speed genetic diagnosis for children and families.
Genoox and Bionano intend to co-sell and co-market the integrated platform for research and future clinical applications when development is completed, likely this summer. Talk to your Bionano Regional Business Manager, or get in touch with us if you’re interested in finding out more, or want to test this platform yourself when it becomes available.