Interpreting Copy-Number Changes: Amplification, Gain, Loss and Deletion

The Vocabulary

A normal diploid genome has two copies of each autosomal gene. Amplification usually means many extra copies (often defined as six or more) focused on a small region, and typically drives strong overexpression, as with HER2 or MYC.

Gain means a modest increase (three or four copies), often across a large region and of less certain significance. Heterozygous loss is one remaining copy; homozygous or biallelic deletion is loss of both copies, which fully removes a gene such as CDKN2A.

Thresholds Are Set by the Laboratory

There is no universal copy-number cut-off. One laboratory may call amplification at copy number six, another at eight, and the reference ploidy assumed for the tumour affects the calculation.

This means an amplification call from one report is not directly comparable to another without knowing the threshold and method.

Purity and Ploidy Distortion

Low tumour purity compresses copy-number signals toward normal, so real amplifications look smaller and homozygous deletions can be missed entirely, masked by the two normal copies contributed by non-tumour cells.

Whole-genome doubling, common in advanced cancers, raises the baseline ploidy, so what looks like a gain may be near-normal for that tumour, and true losses may still leave two copies.

Focal vs Broad, and Loss of Heterozygosity

A focal amplification tightly centred on one gene is more likely to be a driver than a broad gain of a whole chromosome arm that sweeps up many genes.

Copy-neutral loss of heterozygosity, where one parental copy is lost and the other duplicated, keeps the total at two but removes genetic diversity and can unmask a recessive mutation. It is invisible to copy-number analysis that only counts total copies.

Interpretation Notes

A copy-number result should be read with the laboratory's threshold, the estimated purity, and whether the change is focal or broad.

For clinically important calls such as HER2 or MET amplification or CDKN2A deletion, orthogonal confirmation (for example fluorescence in-situ hybridisation) is often used.

Key Takeaways

• ·Amplification (many focal copies) differs from gain (a modest, often broad increase).
• ·Homozygous deletion removes a gene entirely; heterozygous loss leaves one copy.
• ·Thresholds, tumour purity and whole-genome doubling all distort the call.
• ·Focal changes and copy-neutral loss of heterozygosity carry specific meaning.