Bionano Genomics Optical Genome Mapping

Bionano Genomics, Inc. (Nasdaq: BNGO) has started a preclinical evaluation study using optical genome mapping.

The Saphyr system will be used as a research tool to analyze the genomes of couples who have experienced recurrent pregnancy loss or recurrent embryo implantation failure. The study’s objective is to determine whether the improved resolution of OGM, compared to traditional methods, can identify structural rearrangements that could form the basis of downstream targeted testing the embryos before implantation, and thereby potentially lead to improved outcomes of the IVF procedure.

Optical genome mapping (OGM) with the Saphyr® System already provides industry-leading detection of structural variants (SVs) throughout the genome and is used in a wide range of disease applications, including cancer and genetic diseases. A recent patent covers methods for labeling of DNA molecules using sequence-specific probes, which can be used for the more precise characterization of specific parts of the genome in addition to whole-genome analysis. The custom probes can be used to map the limited parts of the genome that are inaccessible to standard labeling methods, such as the centromeres, can help identify highly specific sequences, such as the integration of viral DNA, and can improve the fine mapping of important pathogenic variants such as repeat expansions. Additionally, the use of highly sequence-specific probes allows Saphyr to detect single nucleotide variants in addition to SVs, which currently requires the use of an additional technology such as whole genome sequencing or genotyping arrays.

Large structural variations are responsible for many diseases and conditions, including cancers and developmental disorders. Optical genome mapping with Saphyr detects structural variations ranging from 500 bp to megabase pairs in length and offers assembly and discovery algorithms that far outperform sequencing-based technologies in sensitivity.

For mosaic samples or heterogeneous cancer samples, Saphyr detects all types of structural variants down to 1% variant allele fraction. Saphyr provides this performance typically with a false positive rate of less than 2%. Saphyr also calls repeats and complex rearrangements.

The Saphyr Instrument and high-capacity Saphyr Chip® combine to deliver genome maps at higher speeds.

* Long molecules from 150,000 bp to multi-megabase pairs
* 15 Tbp output per Saphyr Chip for human samples for deep structural variant discovery (5 Tbp per flowcell of molecules larger than 150 kbp)
* Sample to structural variation call or genome scaffolding in as little as 4 days

SOURCES- Bionano Genomics
Written By Brian Wang, Nextbigfuture.com