Pathology & Laboratory Medicine

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Oncomine

Oncomine is a targeted test for the identification of clinically significant somatic mutations including single nucleotide variants (SNVs), insertions and deletions (Indels), gene fusions and copy number alterations (CNAs) from DNA and RNA of 143 cancer-related genes (>2,500 amplicons) in solid tumors, using targeted next generation sequencing (NGS).  The genes interrogated in the assay are categorized by genomic alterations into 73 hot spot genes (with SNVs and Indels), including 49 genes with focal CNAs, such as ERBB2, and 23 genes with known fusions such as ALK and ROS1 in NSCLC.  The test also includes four pairs of 5’, 3’ expression imbalance assays for ALK, ROS1, RET and NTRK1.  In addition, the test provides full coverage of 26 tumor suppressor genes.

The Oncomine Comprehensive panel is able to detect NTRK1, NTRK2 and NTRK3 fusions. Patients with this type of fusion may be eligible for larotrectinib, a recently approved FDA treatment for tropomyosin receptor kinase (TRK) fusion cancers.

Oncomine Fact Sheet
Oncomine FAQ

Specimen Requirements

  1. Formalin-fixed paraffin embedded (FFPE) specimens
    1. One H&E Slide and 15-20 Unstained sections are required
    2. The minimum amount of neoplastic cellularity acceptable is 20%
  2. Fixed Fine Needle Aspiration (FNA) specimen
    1. One H&E Slide and 15-20 Unstained sections from cell block are required
    2. The minimum amount of neoplastic cellularity acceptable is 20%
  3. CytoLyt Solution
    1. Cells suspended in CytoLyt or PreservCyt solution
    2. Preserved at room temperature no longer than 8 days

Ordering the Test

The Oncomine Comprehensive Mutation Panel is available in Epic and can be ordered by an Oncologist. A Pathologist or Cytopathologist can also order the test directly through CoPath.

Disclaimer

The Oncomine Comprehensive Test was developed and its performance characteristics was determined by the Clinical Genomics Laboratory, Englander Institute for Precision Medicine/Department of Pathology and Laboratory Medicine at Weill Cornell Medicine/New York-Presbyterian Hospital; and approved by the New York-State Department of Health (NYS-DOH). This method has not been cleared by the Food and Drug Administration (FDA). The FDA has determined that such clearance or approval is not necessary.

Variants of uncertain origin (germline versus somatic origin) cannot be determined unequivocally in this test, such that germline alterations are not reported. If a possible pathogenic germline mutation (inherited) is suspected, then counselling by a board certified genetic counselor will be recommended in note.

Weill Cornell Medicine Pathology & Laboratory Medicine 1300 York Avenue New York, NY 10065 Phone: (212) 746-6464 Fax: (212) 746-8192