Test Overview
Optical Genome Mapping (OGM) analysis is performed using the Bionano Saphyr optical genome mapping system. Ultra-high-molecular-weight DNA (>150 kb) is isolated from blood and bone marrow aspirate samples. DNA is fluorescently labeled at specific sequence motifs (CTTAAG), linearized, and imaged. The resulting image data are processed to produce maps of individual DNA molecules, which are computationally aligned to the GRCh38/hg38 genome reference to generate a consensus genome map for data analysis.
Analysis is performed using the Bionano Variant Intelligence Applications (VIA) in conjunction with Bionano Access. Chromosomal events such as deletions, duplications, and insertions greater than 10 kb involving clinically significant cancer-related genes, or gains or losses greater than 1 Mb outside of clinically significant oncology regions are reported. Recurrent or clinically relevant structural variants, such as fusions, translocations, and inversions, are also reported. Copy number variants reported in population databases (Database of Genomic Variants, gnomAD database, or Bionano control database) are excluded.
Optical Genome Mapping (OGM) is intended for the cytogenomic evaluation of hematologic malignancies. It is designed to identify structural variants including translocations, inversions, insertions, deletions, and duplications, at a high genomic resolution as well as large copy number gains and losses.
In hematological malignancies, the OGM assay will complement karyotype analysis and, in many cases, will replace reflex FISH assays and chromosomal microarray analysis. By providing a detailed view of chromosomal architecture, OGM detects recurrent gene rearrangements (for examples, RUNX1T1::RUNX1, CBFB::MYH11, PML::RARA, GATA2::MECOM, BCR::ABL1, ETV6::RUNX1, IGH::MYC), and large copy number aberrations (for examples, hyperdiploidy, deletion of 5q and 7q, complex genomic aberrations). It is particularly useful for malignancies that are characterized by cryptic rearrangements or enhancer hijacking that are often difficult to detect by G-banded chromosome analysis or targeted assays. Its ability to detect both known and novel genomic aberrations makes it a valuable tool for initial diagnosis and at the disease progression or relapse.
Interpretive report provided.
* Reference ranges may change over time. Please refer to the original patient report when evaluating results.
While Optical genome mapping assay is designed to detect a broad spectrum of genomic variants in hematological malignancies, it may not identify all variant types. Specifically, it does not detect single-nucleotide variants, small deletions or duplications, tetraploidy, balanced Robertsonian translocations, or variants with breakpoints located within poorly covered areas such as centromeres, telomeres, repetitive regions, or heterochromatin-rich regions. It also has limited detection for copy-neutral loss of heterozygosity. Additionally, this method is not validated for the detection of measurable residual disease or small clones. Copy number variants present in less than 20% of the cell population, or structural variants occurring below 5% allele fraction, may not be reliably detected.
Failure to detect an alteration at any locus does not exclude a specific diagnosis. Results should be correlated with clinical, pathological and other laboratory findings.
Test Details
Specimen Requirements
Specimen transport should be arranged so that the specimen is received by MLabs the same day it is collected. Call for a STAT courier if necessary. Collect specimen in a lavender top (preferred) or green top (sodium heparin-acceptable) tube. Invert the tube several times to prevent clotting. Send the specimen intact at room temperature as soon as possible. DO NOT CENTRIFUGE. Include pertinent medical finding and diagnosis. Most insurance carriers require prior authorization for payment. Testing will not begin until insurance prior authorization is received, it is confirmed that prior authorization is not required, or the patient has agreed to pay out of pocket. A completed Michigan Medicine Request form is required and is available by calling 800-862-7284 or online: hematopathology-consult-requisition.docx.
2–3 mL blood or bone marrow
1 mL blood or bone marrow (minimum 1,000,000 cells)
Additional Information
If necessary, reflex FISH or Chromosomal Microarray Analysis will be performed at an additional charge, to confirm, clarify, or further characterize the Optical Genome Mapping results. By ordering this test, the clinician acknowledges that additional reflex testing may be performed and billed separately if indicated. Further, the clinician acknowledges that informed consent has been obtained from the patient, as required by applicable state or federal laws and the ordering clinician has authorization from the patient permitting MLabs to report the test results to the ordering clinician.