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EXaCT-1 (Whole-Exome Sequencing)

The EXaCT-1 assay provides an unbiased, exploratory view of more than 22,000 genes in both healthy and malignant cells, allowing molecular pathologists to find alterations in the cancer-development process in unexpected regions of an exome. This type of test, known as whole-exome sequencing, can be effective for advanced-stage patients for whom other treatments have failed because it reveals mutations that less comprehensive tests may not uncover. In practice, this means, for example, that a patient with bladder cancer, whom EXaCT-1 shows to share a mutation associated with breast cancer, might benefit from a drug typically prescribed to fight the latter type of tumor.

Specimen Requirements

A surgical pathology and/or cytology report and completed requisition form must accompany all specimens.

Solid Tumor Malignancies

For solid tumor malignancies, both a tumor sample and a normal blood sample are required. In the majority of cases, a blood draw can be scheduled through Epic and sent to the lab. However, for some patients, a different type of non-tumorous sample, such as a buccal swab, may be required.

  • Tumor requirements: 20 unstained slides and one Hematoxylin and Eosin (H&E) stain – the minimum amount of neoplastic cellularity should be at least 20 percent.
  • Blood requirements: 2-3 milliliters of whole blood in a lavender-top EthyleneDiamineTetraacetic Acid (EDTA) tube.
OR
Hematologic Malignancies

For hematologic malignancies – including leukemia, myelodysplastic syndromes, myeloproliferative neoplasms, lymphomas and multiple myeloma – we require the following sample types:

Tumor requirements (select one of the following):

  • Formalin-Fixed Paraffin-Embedded (FFPE) slides
    • 20 unstained slides and one H&E recut slide, with a minimum amount of plastic cellularity greater than 20 percent
  • Peripheral blood
    • 2-5 milliliters collected in one lavender-top EDTA tube, with tumor content greater than 20 percent and diagnosis confirmed with an accompanying flow cytometry report
  • Bone Marrow Aspirate
    • 1-3 milliliters collected in one lavender-top EDTA tube

Normal (control) requirements (select one of the following):

  • Buccal (cheek) swab
    • Buccal swab kits can be obtained by contacting the Weill Cornell Medicine Clinical Genomics Laboratory directly.
  • Peripheral blood
    • 2-5 milliliters collected in one lavender-top EDTA tube
    • Blood should only be used as a control if no tumor cells are present in the blood sample.

Disclaimer

EXaCT-1 was developed and tested in Englander Institute for Precision Medicine (EIPM) and NewYork-Presbyterian (NYP) Hospital laboratories. EXaCT-1 has not been approved by the Food and Drug Administration (FDA). The FDA has determined that such approval is not necessary. EXaCT-1 may be used for clinical purposes and should not be regarded as only experimental or investigative. The lack of a given genetic alteration in this report does not necessarily indicate the absence of the alteration in a tumor, as technical aspects of the assay, including inadequate coverage of specific genes, limit the data that can be acquired in certain genetic regions. Alterations that occur in the germ line are not reported. If a possible pathogenic (inherited) germ line mutation is suspected, counseling from a board-certified genetic counselor will be recommended.

Cancer Type: Solid tumor and hematologic malignancies

Indication: Comprehensive profile of all genes within cancer cells – EXaCT-1 facilitates a more complete understanding of a patient’s cancer through evaluation of an entire tumor exome.

Turnaround: 3-4 weeks

# of Genes: ~22,000

Status: New York state-approved

Resources

FDA-Approved, Targeted Therapies
Genomic Testing Pre-Authorization Form
Sample Report
Solid Tumor Tissue Requirements

Faculty

Wei Song
Wei Song, M.D., Ph.D.
  • Director
Phone: (646) 962-3824
Fax: (646) 962-0199