Optical Genome Mapping (OGM) detects structural variations in an unbiased manner and at much higher sensitivities than sequencing-based technologies, and routinely at 5% variant allele fraction. OGM uncovers large structural variations beyond what short- and long-read sequencing can see. The workflow is simple, and it starts with ultra-high molecular weight DNA isolation from blood, cells, tissue or tumor biopsies. A single enzymatic reaction places 500,000 fluorescent labels all throughout the genome at a specific sequence motif occurring approximately 20 times per 100 kbp in the human genome. The long, labeled DNA molecules are linearized in nanochannel arrays on a Saphyr chip ® and imaged in an automated manner by the Saphyr ® Instrument. Changes in patterning or spacing of the labels are detected automatically, genome-wide, to call all structural variants. - Variant allele fraction detection: 5% - Coverage per sample: 400X - Insertions/deletions: 500 bp for diploid genomes; 5 kbp for mosaic sample - Balanced and unbalanced translocations: Larger than 50 kbp - Inversions: Larger than 30 kbp - Duplications: Larger than 30 kbp OGM Consolidates Karyotyping, FISH, and CMA in a Single Workflow. Identification of complex rearrangements in cancer often requires a combination of approaches, which are typically performed sequentially. This sequential approach manages costs, but increases the turnaround time and complicates the understanding of the genetic makeup of the sample. A leukemia sample presented a challenging karyogram, necessitating chromosomal microarray as a complement to validate t(1;2). Suspicion of a previously missed t(5;14) called for a FISH analysis. Results from karyotyping and FISH were inconclusive since the acceptor chromosome couldn't be clearly identified. The two events were captured by OGM in a single experiment and benign structural variants were automatically filtered out without complex pipelines. OGM Identifies Mutation Signatures and Brings Order Without Complex Pipelines. Cancer samples often display a high number of structural variants, and the limitations of the short-read length of NGS are particularly detrimental for correctly reconstructing these chained fusion events. In this patient-derived breast cancer cell line, a consensus map resulting from the alignment of dozens of molecules spanning the region allowed OGM to identify a succession of a translocation, deletions and an inversion missed by short- and long-read sequencing. The ability to stratify patient samples based on mutational profiles usually requires extensive bioinformatic data curation downstream of sequencing. In a hepatocellular carcinoma study, our built-in pipeline automatically provides enough information to distinguish samples with or without a replication stress signature. OGM can rapidly collect several thousand folds of coverage of a human genome, allowing for the detection of undesired rearrangements. Combined with NGS, OGM Provides a Comprehensive Understanding of Cancer Events, From SNVs to Multi Mega Base Pair Structural Variations. For Research Use Only. Not for use in diagnostic procedures.
