Test Overview
Test Methodology

This Cancer Cytogenomic Array assay is performed using the Thermo Fisher OncoScan platform. The assay utilizes Molecular Inversion Probe (MIP) technology, which is optimized for highly degraded FFPE samples (probe interrogation site of just 40 base pairs). For copy numbers the assay has a resolution of 50-100 kb in selected 900 cancer genes and of 300 kb outside of the cancer genes. Gains and losses that include a known clinically significant cancer gene, or are greater than 3Mb outside clinical oncology significant regions, and loss of heterozygosity greater than 10Mb are reported. Results are analyzed and interpreted using Thermo Fisher Chromosome Analysis Suite software (ChAS).

Test Usage

Cancer Cytogenomic Array-FFPE tissue assay detects DNA copy number gains (including amplification) and losses as well as regions of copy neutral loss of heterozygosity (CN-LOH). It is often useful in the diagnosis, classification, and prognostic evaluation of malignant tumors. This array has been validated in central nervous system lesions, and gonadal or extragonadal germ cell tumors (i(12p) assessment by Cancer Cytogenomic Array-FFPE Tissue). At least 30% malignant cells must be present in the sample submitted for Cancer Cytogenomic Array -FFPE tissue assay.

Reference Range *

Interpretive report provided.
*Reference ranges may change over time. Please refer to the original patient report when evaluating results.

Test Limitations

Although Cancer Cytogenomic Array – FFPE tissue is a powerful diagnostic tool for the evaluation of chromosomal copy number changes, this assay will not detect balanced chromosomal aberrations, imbalance of regions not represented on the microarray, point mutations, small gains or losses below the resolution of the assay, or other types of mutations such as epigenetic changes. Although copy number changes present at 20% of cells can generally be detected using a SNP array, the quality of solid tumor specimens is very variable. Therefore, this test requires 30% or greater tumor burden in the specimen. Interpretation of Cancer Cytogenomic Array results can be complicated by the detection of constitutional changes that may or may not be related to the malignancy. This may warrant genetic testing of a peripheral blood sample, and referral to a clinical geneticist for further evaluation and counseling.

Test Details
Days Set Up
Monday - Friday, 8:00am - 4:00pm
Analytic Time

10-21 days

Soft Order Code
MiChart Code
Cytogenetics, Cancer Cytogenomic Array-FFPE Tissue
  • i(12p) assessment by Cancer Cytogenomic Array
Specimen Requirements
Cancer Cytogenomic Array-FFPE Tissue assay should not be ordered for follow-up studies to determine remission status or presence of minimal residual disease.
Normal Volume
Ten consecutive, unstained, unbaked FFPE tissue rolls cut at 10-micron thickness sections placed on positively charged slides are required. If the surface of the tissue section is above 0.5 cm2, 5 tissue rolls at 10-micron thickness are sufficient. One serial H&E is also required to assess specimen adequacy and to mark the tumor area for DNA extraction.
Rejection Criteria
-Samples with less than 30% malignant cells or the tumor area is less than 1mm2 are not suitable for CGH.
-Samples with total DNA yield less than 80ng and concentration less than 12ng/ µl, may be rejected due to the minimum DNA input requirements of CGH.
Additional Information

Appropriate FISH testing on a separate sample may be performed at an additional charge to confirm, clarify, or further characterize the Cancer Cytogenomic Array results if necessary. By ordering this test the clinician acknowledges that additional reflex testing will be performed and billed at a separate additional charge if indicated. Also, by ordering this test the clinician acknowledges that informed consent has been obtained from the patient as required by applicable state or federal laws.

CPT Code
Fee Code
NY State Approved