This microarray 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 detecting malignant conditions in FFPE tissues which usually generate degraded DNA and low DNA yield. At least 30% malignant cells must be present in the sample submitted for Chromosomal Microarray Analysis for Tumor assay.
Interpretive report provided.
Although SNP 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. 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 the results can be complicated by the detection of mosaic changes that due to mixture of tumor cells with normal cells, which will decrease the copy number aberration density. In some cases, results may suggest that the patient may benefit from referral to a clinical geneticist for further evaluation and counseling.
Tissue rolls: If examination of a representative H&E tissue section reveals that more than 50% of the cells are tumor cells, 10 FFPE tissue rolls cut at 10-micron thickness in a clean 1.5 mcL tube are required. If the surface of the tissue section is above 0.5 cm2, 5 tissue rolls at 10-micron thickness are sufficient. For cases with very small amounts of tissue, it may be necessary to cut more than ten 10-micron sections to ensure the presence of sufficient material from which to extract DNA. Avoid exhausting the FFPE block whenever possible. One serial H&E is also obtained to assess specimen adequacy. Cases in which the percentage of tumor cells is less than 30% or the tumor area is less than 1mm2 are not suitable for CGH.
Unstained slides: If examination of a representative H&E tissue section reveals that less than 50% of the cells are tumor cells, 10 FFPE serial unstained sections at 10-microns thickness on regular slides and one H&E slide are required. The tumor area is marked by a certified pathologist to ensure a minimum of 30% tumor purity in the sample. While 10-micron thick sections are preferred, 4-micron sections are acceptable. The tissue in the marked area is micro-dissected from the slide with a sterile scalpel and placed in a 1.5 mL tube. Cases in which the percentage of tumor cells is less than 30% in the area to be micro-dissected or the tumor area is less than 1mm2 are not suitable for CGH.
DNA yield: Samples with total DNA yield and concentration above 80ng and 12 ng/mcL, respectively, are acceptable. Samples with total DNA yield less than 80 ng and concentration less than 12 ng/mcL will be rejected due to the minimum DNA sample input and volume requirements of CGH. For those samples with total DNA yield below 80 ng but with concentration less than 12 ng/mcL, a concentration step is included in the protocol.
Concurrent chromosome analysis should be sent for all the samples requesting Chromosomal Microarray Analysis for Tumor.