Test Overview
Test Methodology

This Cancer Cytogenomic Array assay is performed using the Affymetrix Cytoscan HD platform. This array contains more than 2.6 million copy number markers, including 750,000 SNPs, with a median spacing of 0.88 kb within genes. Patient DNA is isolated, amplified, enzymatically fragmented, and hybridized to oligonucleotide probes. The array is washed, scanned, and the results are analyzed and interpreted using Affymetrix Chromosome Analysis Suite software (ChAS).

Test Usage

Cancer Cytogenomic Array assay detects DNA copy number gains (including amplification) and losses as well as regions of copy neutral loss of heterozygosity (CN-LOH) by SNP analysis. This assay is particularly useful for malignant conditions with a low mitotic index and when limited material is available for standard cytogenetic analysis. At least 30% malignant cells must be present in the sample submitted for Cancer Cytogenomic Array 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 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, or point mutations. A karyotype or FISH test is more appropriate when a translocation or inversion is suspected. Also, chromosome or FISH analysis is more appropriate if a STAT result is required. 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
Analytic Time

3 weeks

Soft Order Code
CGATU
Synonyms
  • CGATU
  • Array CGH (aCGH), Tumor
  • Microarray CGH, Tumor
  • Chromosomal Microarray Analysis, Tumor
  • Array for Neoplasia, Tumor
  • Cytogenomic Microarray, Neoplasia
  • Cancer Cytogenomic Microarray, Tumor
  • SNP Array, Tumor
  • Cancer Array
Laboratory
Cytogenetics
Section
Cytogenetics
Specimen Requirements
Collection Instructions

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 tumor specimen using aseptic technique. Place tissue in Chromosome Media in a Nalgene cryogenic vial, available from MLabs. Specimen must be shipped at at room temperature and received by the laboratory within 24 hours of collection. Do not allow specimen to overheat or freeze. Alternatively, fresh specimen can be frozen at less than or equal to -20 degrees C and shippped on dry ice by overnight courier. Small samples with insufficient amount of DNA or necrotic samples with greatly degraded DNA are not acceptable. 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 and Consent for Genetic Testing form is required and is available by calling 800-862-7284 or online: https://mlabs.umich.edu/sites/default/files/2020-01/file/pci-mmgl_infor….

Rejection Criteria
Small samples with insufficient amount of DNA or necrotic samples with greatly degraded DNA are not acceptable. At least 30% malignant cells must be present in the sample submitted for Cancer Cytogenomic Array assay.
Contraindications
Cancer Cytogenomic Array should not be ordered for follow-up studies to determine remission status or presence of minimal residual disease.
Normal Volume
3 cm(3)
Minimum Volume
0.5 cm(3) or 25 mg
Additional Information

Concurrent chromosome analysis should be sent for all the samples requesting Cancer Cytogenomic Array assay. Appropriate FISH testing on a separate sample will 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.

Billing
CPT Code
81277
Fee Code
EA026
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