Chromosome Arm Aneuploidy Score

Overview

A quantitative per-sample metric that counts the number of chromosome arms showing broad somatic copy-number alteration (gain or loss) relative to the sample’s euploid level. The score ranges from 0 to 39 (summing altered p and q arms of non-acrocentric autosomes plus q arms of chromosomes 13–15, 21, and 22). Arm-level calls are derived from ABSOLUTE-segmented copy number using a Gaussian mixture model with BIC-based cluster selection (2–9 clusters); arms where the mean SCNA spans ≥80% of arm length are called “altered,” ≤20% are called “normal,” and intermediates are left uncalled.

Used by

• Defined and applied to 10,522 TCGA pan-cancer tumors across 33 cancer types; score correlates almost perfectly with fraction of genome altered (Spearman ρ = 0.975); reveals TP53 mutation as the only positive outlier in a pan-cancer multivariable linear model; shows cancer-type-specific clustering by arm-level pattern (squamous cluster: chr_3p loss + chr_3q gain) PMID:29622463

Notes

• The score is intentionally restricted to broad arm-level events and excludes focal SCNAs, departing from some other aneuploidy definitions in the literature.
• Score values range from 0 (THCA mean 0.87) to ~18.7 (TGCT mean).
• Derived from Affymetrix SNP 6.0 + ABSOLUTE data; applying to other platforms requires re-derivation.
• Tetraploid samples (18 cases) are assigned score 0 as a conservative choice.

Sources

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