Karyotypic Determinants of Chromosome Instability Figure 5. Association of chromosome copy number imbalance with CIN. (A) Enrichment of strains belonging to the combined MU and HU classes of CIN relative to the S class (left) or to the HU class of CIN relative to the combined S and MU classes (right) among aneuploid strains displaying a particular chromosome copy number imbalance, calculated for each non-redundant pair of chromosomes. The enrichment is color- coded based on p-values calculated by means of Hypergeometric tests. Darker colors indicate more significant enrichment of strains belonging to the S class of CIN (left) or HU class of CIN (right) among strains with a non-1 copy number ratio between a given pair of chromosomes. (B) Diagram illustrating the experimental design for the assessment of the relationship between CIN and MAD2:MAD1 ratio in 56 freshly generated aneuploid strains from isogenic triploid sporulation. (C–D) Frequency of aneuploid strains with stable or unstable ploidy grouped by their MAD2:MAD1 ratio. Ploidy-stable strains (black histograms) were identified on the basis of their low level of ploidy variation among single colonies analyzed by FACS; ploidy-unstable strains (white histograms) were identified on the basis of high ploidy variation among single colonies. MAD2:MAD1 ratios were determined by qPCR and are indicated on the x-axis. P-values at the top of (C–D) graphs refer to statistical association between the stability category and the MAD2:MAD1 ratio category by means of a Fisher’s exact test. Aneuploid strains were divided into all four possible MAD2:MAD1 ratio classes (C) or based on MAD2:MAD1 ratio equal or not equal to 0.5 (D). doi:10.1371/journal.pgen.1002719.g005 by some general property of being aneuploid per se but rather by determinants associated with specific aneuploid karyotypes. An advantage of our study is the carefully controlled genome variability among the strains analyzed. Because all aneuploid strains were derived from the same homozygous triploid parent and underwent minimal passage before their analysis [15], the different strains only differed in chromosome stoichiometry, minimizing the possibility that the observed CIN was due to other genetic variations or aberrations between different strains. Another advantage of our study was that CIN was assessed by examination of a wide range of spontaneously occurring karyo- typic changes that include copy number gains and losses of native PLoS Genetics | www.plosgenetics.org 9 May 2012 | Volume 8 | Issue 5 | e1002719