Table 1 Scores and indices used to quantify aneuploidy
From: Aneuvis: web-based exploration of numerical chromosomal variation in single cells
Method | Equation | Support | %-based? | Reflects magnitude of copy number changes? | Reflects variability in chromosomal states? | Meaning and Considerations |
|---|---|---|---|---|---|---|
Instability index (I) | \( I=\left(\frac{\sum \limits_{t=1}^T{k}_t}{T}\right)\ast 100 \) | I ∈ [0, ∞) | No | No | Yes | Calculates the sum of the percentage of abnormal chromosome counts across each chromosome. |
Consider: I may increase with the # of chromosomes measured. | ||||||
ANCA (A) | \( A=\left(\frac{\sum \limits_{n=1}^N{q}_n}{n}\right) \) | A ∈ [0, ∞) | No | No | No | ANCA = Average Number of Copy Number Alterations per cell. |
Consider: A will ↑ as the # of measured chromosomes ↑s. | ||||||
Normalized ANCA (AN) | \( AN=\left(\frac{\sum \limits_{n=1}^N{q}_n}{T\ast n}\right) \) | A ∈ [0, ∞) | No | No | No | AN is the ANCA score normalized for differences in number of chromosomes measured per experimental type (eg FISH vs sc-WGS). |
Aneuploidy score (D) | \( D=\frac{1}{TN}\sum \limits_{n=1}^N\sum \limits_{t=1}^T\mid {c}_{n,t}-{e}_t\mid \) | D ∈ [0, ∞) | No | Yes | No | D increases with increased chromosome number. |
Consider: Even a few cells with very large numbers of chromosomes will cause D to ↑ (not so with H) | ||||||
Heterogeneity score (H) | \( H=\frac{1}{TN}\sum \limits_{t=1}^T\sum \limits_{f=0}^{S-1}f\bullet {m}_{f,t} \) | H ∈ [0, ∞) | No | No | Yes | Increases with greater ‘spread’ in the number of observed chromosomal states |
Consider: H is maximized when each cell has a different number of chromosomes, regardless of absolute # of chromosomes. | ||||||
Ploidy proportion | PA + PD + PP = 1 | PA, D, P ∈ [0, 1] | Yes | No | Yes | PD = 1, PA = 0, PP = 0 when population is diploid. |