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Tensor GSVD of Patient- and Platform-Matched Tumor and Normal DNA Copy-Number Profiles Uncovers Chromosome Arm-Wide Patterns of Tumor-Exclusive Platform-Consistent Alterations Encoding for Cell Transformation and Predicting Ovarian Cancer Survival

Fig 2

Tumor-exclusive and platform-consistent DNA copy-number alterations (CNAs) correlated with ovarian serous cystadenocarcinoma (OV) patients’ survival.

(a) Plot of the first 6p+12p tumor arraylet describes a pattern of tumor-exclusive and platform-consistent co-occurring CNAs across the combination of the two chromosome arms 6p+12p. The probes are ordered, and their copy numbers are colored according to each probe’s chromosomal band location. Segments (black lines) amplified and deleted include most known OV-associated CNAs that map to 6p+12p (black), including an amplification of KRAS and a deletion of PRIM2. CNAs previously unrecognized in OV (red) include a deletion of the p38-encoding MAPK14, and p21-encoding CDKN1A, and an amplification of RAD51AP1, a deletion of TNF, and focal amplifications of ASUN, ITPR2, and the 5’ ends of isoforms a and e, and exons 5 and 6 of SOX5. A high 6p+12p arraylet correlation is significantly correlated with a patient’s shorter survival time. (b) Plot of the first 6p+12p x-probelet describes the classification of the discovery set of patients into two groups of high (blue) and low (red) coefficients. A high 6p+12p x-probelet coefficient is significantly and robustly correlated with a patient’s shorter survival time. (c) Raster display of the 6p+12p tumor profiles, where medians of the profiles of the same patient measured by the two platforms were taken, with relative gain (red), no change (black), and loss (green) of DNA copy numbers. (d) Plot of the first 7p tumor arraylet describes a pattern of CNAs across the chromosome arm 7p. CNAs previously unrecognized in OV (red) include a focal deletion of RPA3 and an amplification of POLD2. A high 7p arraylet correlation is significantly correlated with a patient’s longer survival time. (e) Plot of the first 7p x-probelet describes the classification of the discovery set of patients into two groups of high (red) and low (blue) coefficients. A high 7p x-probelet coefficient is significantly and robustly correlated with a patient’s longer survival time. (f) Raster display of the 7p tumor profiles. (g) Plot of the first Xq tumor arraylet. CNAs previously unrecognized in OV (red) include a focal deletion of PABPC5 and an amplification of BCAP31. A high Xq arraylet correlation is significantly correlated with a patient’s longer survival time. (h) Plot of the first Xq x-probelet describes the classification of the discovery set of patients into two groups of high (red) and low (blue) coefficients. A high Xq x-probelet coefficient is significantly and robustly correlated with a patient’s longer survival time. (i) Raster display of the Xq tumor profiles.

Fig 2

doi: https://doi.org/10.1371/journal.pone.0121396.g002