In DNA microarray (gene chip) technology, thousands of oligonucleotide probes are spotted on a solid surface. Patient mRNA is reverse-transcribed to cDNA, labeled with fluorescent dyes, and hybridized to the array. In a two-color comparative genomic hybridization (aCGH) for copy number variation detection, tumor DNA is labeled red and normal control DNA is labeled green. A region showing red:green ratio of 2.0 indicates what?

• A Two copies of the region in the tumor vs. one copy in normal (ratio 2:1)
• B Homozygous deletion of the region in normal tissue
• C Equal copy numbers in tumor and normal; ratio of 2.0 reflects dye labeling efficiency difference
• D Two extra copies of the region in the tumor (4 total copies vs. 2 in normal) ✓

Explanation

In two-color aCGH, a red:green fluorescence ratio of 2.0 means the tumor has twice as many copies of that genomic region compared to normal diploid reference DNA. Normal diploid cells have 2 copies, so ratio 2.0 corresponds to 4 copies in the tumor (amplification). A ratio of 1.0 = equal copy number; 0.5 = loss of one copy (3 normal : 1 normal, or hemizygous deletion in tumor); 0 = homozygous deletion in tumor. Amplification ratios >2 (log2 ratio >1) in aCGH indicate high-level amplification (e.g., ERBB2/HER2 amplification in breast cancer shows ratios >3-4). This copy number analysis is essential in cancer genomics for identifying oncogene amplifications and tumor suppressor deletions.

Reference: Harper's Illustrated Biochemistry, 32nd ed.

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Written and medically reviewed by the StethoPrep medical team.