The OGM workflow starts with mega-base size DNA isolation. A single enzymatic reaction labels the genome at a specific sequence motif occurring approximately 15 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. Using pairwise alignments, the molecules are assembled into local maps or whole genome de novo assemblies. Changes in patterning or spacing of the labels are detected automatically, genome-wide, to call all structural variants.
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Revolutionizing
Cytogenomics
Detecting broken, missing, rearranged, or extra chromosomes can diagnose disease and define treatment options, but traditional cytogenetic methods have limited resolution and speed. Optical genome mapping (OGM) detects all CNVs, chromosomal aberrations and structural variants and consolidates the traditional cytogenetic assays into one single workflow.
Meet the Saphyr System: Your New Cyto Lab
Optical genome mapping with the Saphyr® System can detect all classes of structural variant at high sensitivities, even those present at low allele fractions in heterogenous cancer samples, in an unbiased genome-wide manner. This modern tool has revolutionized cytogenomics by showing a 100% concordance to traditional methods – array CGH, karyotyping and FISH – in multiple studies. With the Saphyr system, you can easily consolidate 3 assays into 1 to get results in as few as 4 days* with a single streamlined workflow.
*For human samples collected at 100x and analyzed through the de novo assembly pipeline.
Bionano offers a simple, reliable method for assessing chromosomal aberrations at a much higher resolution.
Data Examples
OGM demonstrated 100% concordance with karyotyping, FISH, and chromosomal microarray in constitutional disorders in two studies appearing in the July 2021 issue of the American Journal of Human Genetics (AJHG).
The authors in these back-to-back publications describe OGM as a better alternative to traditional cytogenetic assays for both inherited genetic disease and hematologic malignancy applications since it consolidates multiple antiquated methods requiring manual integration for interpretation into a single workflow with higher resolution for detection of all classes of structural variants.
A consortium led by Dr. Brynn Levy at Columbia, who validated chromosomal microarray for cytogenetic use, is leading an AML clinical benchmark study. The consortium includes Penn State University, Harvard University, The Pathgroup, Mayo Clinic, University of Washington, and others.
Dr. Alex Hoischen (RUMC), a pioneer in bringing new technologies to the clinic, and Dr. Laila El Khattabi (Cochin Hospital Paris) are leading a group of European labs performing a clinical validation on constitutional disorder testing.
Dr. Guillermo Garcia-Manero, head of MD Anderson’s AML & MDS Moon Shot Program and Dr. Rashmi Kanagal-Shamanna, director of the hematopathology microarray facility, are performing a clinical benchmark study on patients with Myelodysplastic Syndrome.
Dr. Ravi Kolhe from Augusta University who clinically validated several diagnostic assays is developing a Lab Developed Test for cancer based on leukemia and glioblastoma samples.
Dr. Eddy Maher from NHS Lothian in Edinburgh, who introduced chromosomal microarray in the UK clinics, is running a clinical validation for cytogenetic testing and NHS certification.
Data Examples
The OGM workflow starts with mega-base size DNA isolation. A single enzymatic reaction labels the genome at a specific sequence motif occurring approximately 15 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. Using pairwise alignments, the molecules are assembled into local maps or whole genome de novo assemblies. Changes in patterning or spacing of the labels are detected automatically, genome-wide, to call all structural variants.

OGM demonstrated 100% concordance with karyotyping, FISH, and chromosomal microarray in constitutional disorders in two studies appearing in the July 2021 issue of the American Journal of Human Genetics (AJHG).
The authors in these back-to-back publications describe OGM as a better alternative to traditional cytogenetic assays for both inherited genetic disease and hematologic malignancy applications since it consolidates multiple antiquated methods requiring manual integration for interpretation into a single workflow with higher resolution for detection of all classes of structural variants.
A consortium led by Dr. Brynn Levy at Columbia, who validated chromosomal microarray for cytogenetic use, is leading an AML clinical benchmark study. The consortium includes Penn State University, Harvard University, The Pathgroup, Mayo Clinic, University of Washington, and others.
Dr. Alex Hoischen (RUMC), a pioneer in bringing new technologies to the clinic, and Dr. Laila El Khattabi (Cochin Hospital Paris) are leading a group of European labs performing a clinical validation on constitutional disorder testing.
Dr. Guillermo Garcia-Manero, head of MD Anderson’s AML & MDS Moon Shot Program and Dr. Rashmi Kanagal-Shamanna, director of the hematopathology microarray facility, are performing a clinical benchmark study on patients with Myelodysplastic Syndrome.
Dr. Ravi Kolhe from Augusta University who clinically validated several diagnostic assays is developing a Lab Developed Test for cancer based on leukemia and glioblastoma samples.
Dr. Eddy Maher from NHS Lothian in Edinburgh, who introduced chromosomal microarray in the UK clinics, is running a clinical validation for cytogenetic testing and NHS certification.
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Optical genome mapping using Saphyr® reveals what’s missing in your research. Rapidly identify genome variation like never before with the high-throughput Saphyr system.
Built using proprietary Nanochannel technology, Bionano Chips for the Saphyr® and Irys® systems linearize DNA, enabling high-speed, high-throughput optical genome mapping and structural variation detection for a variety of applications including human and clinical research.
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