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Platform-Independent Genome-Wide Pattern of DNA Copy-Number Alterations Predicting Astrocytoma Survival and Response to Treatment Revealed by the GSVD Formulated as a Comparative Spectral Decomposition

Fig 3

GBM genome-wide pattern of co-occurring CNAs previously uncovered by the GSVD of GBM tumor and normal profiles.

(a) Plot of the second most GBM tumor-exclusive tumor arraylet, which was previously uncovered by the GSVD [8], describes a genome-wide pattern of co-occurring CNAs across 212,696 Agilent probes. The GBM pattern, which encompasses the LGA pattern (Fig 2), consists of LGA-shared (black) and GBM-specific (blue) CNAs, including, e.g., gains of segments on chromosome 1 containing MDM4 and AKT3, respectively. (b) Both LGA-shared and GBM-specific CNAs are visible across the 8,102 Affymetrix-matched Agilent probes, even though these are <4% of the probes that constitute the GBM pattern. (c) The LGA-shared CNAs, e.g., in MDM4, are visible across the 4,697 Affymetrix-matched consistently-aberrated Agilent probes. (d) The GBM-specific CNAs, e.g., in AKT3, are visible across the 3,405 remaining probes.

Fig 3