OncoSeq - NGS Panel for Solid Tumors

Test Details

OncoSeq is a targeted NGS panel designed to assist in diagnosis, prognostication and treatment of adult cancers, e.g. lung adenocarcinoma, colorectal cancer and melanoma. It allows for the simultaneous analysis of a broad spectrum of genetic alterations, including point mutations in most commonly mutated hot spots of 28 genes and for copy number alterations in 23 genes in a single workflow. For the full list of hot spots tested by the panel please download the OncoSeq hot spots document.

Genes Tested

AKT1 CDKN2A ERBB4 GNA11 IDH1 MET PTEN
ALK CTNNB1 FGFR1 GNAQ IDH2 NRAS SMAD4
ATM EGFR FGFR2 GNAS KIT PDGFRA TP53
BRAF ERBB2 FGFR3 HRAS KRAS PIK3CA VHL

Methodology

OncoSeq NGS Panel is performed on DNA isolated from formalin-fixed, paraffin-embedded (FFPE) or fresh/frozen tumor tissue. For enrichment of tumor cell population, all surgically removed tumor specimens are microdissected from unstained slides under the microscope with H&E guidance. Specimens with a minimum of 20-50% of tumor cells or at least 300 tumor cells in a microdissection target are accepted for analysis.

Using Ion AmpliSeq technology (Life Technologies) genomic DNA is used for multiplex PCR amplification of 128 amplicons, which target hotspots in 28 key cancer-related genes.

Amplicons are barcoded, purified and ligated with specific adapters. A final check of library preparation is performed using the 2200 Tapestation. The Ion One Touch2 and One Touch ES are used to prepare and enrich templates and enable testing via Ion Sphere Particles on a semi-conductor chip. Next generation bidirectional sequencing was performed on the Ion Torrent Personal Genome Machine (PGM) or Ion Proton and analyzed with the Torrent Suite Software. Variant annotation and reporting was performed with Variant Explorer and SeqRepoter software (UPMC). The analytical sensitivity is 3-5% of mutant alleles for detection of mutations. The minimal required sequencing depth is 300x.

  • Input DNA: 10ng

Specimen Requirements and Shipping Instructions

Paraffin embedded tissure sections

  • Tissue should be fixed in formalin and not exposed to decalcification solution. The paraffin block should contain no less than 3 mm area of tumor.
  • Slides should prepared by histology using a specific protocol for cutting molecular sections to avoid contamination of the tissue sections (available upon request).
  • One H&E and 6 unstained sections are required for most of the tests. Ten unstained sections or more are required for some tests (indicated by * in the test menu) or if the tissue is small. Please call the lab if you have questions.
  • Slides should be properly labeled with a block label that matches the surgical pathology specimen number on the surgical pathology report.
  • Slides should be sent ambient temperature in proper storage containers (plastic slide boxes) to protect them during shipment.
  • A surgical pathology and/or cytology report and completed requisition for must accompany all specimens.

Frozen tissue

  • A minimum of 2 x 2 x 2 mm of frozen tissue is required; however, 5 x 5 x 5 mm is optimal.
  • Collection date and time should be stated.
  • Tissue specimen containing at least 50% of tumor cells can be either placed into cryogenic tube and snap frozen in liquid nitrogen, or placed into a tube with preservative solution provided by the Molecular & Genomic Pathology laboratory (request solution from the lab) and frozen at -20° C.
  • Ship overnight on dry ice. A surgical pathology and/or cytology report and completed requisition form must accompany all specimens.

Turnaround Time

7 days

Billing Information List Price

* For insurance or Institutional Price, please call.