A balancing act: how whole-genome doubling and aneuploidy interact in human cancer

Prasad, Kavya; Ben‐David, Uri

doi:10.18632/oncotarget.28374

Cited by 2 publications

(2 citation statements)

References 6 publications

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“…We identified 1,280 significantly co-occurring chromosome arm loss-gain event pairs out of 31,122 possibilities (Fisher exact test, false discovery rate or FDR < 0.05; Table S1 ; Methods ). Our findings are in line with previous work by Prasad et al 65,66 , which examined the TCGA cohort 64 . We find a significant overlap between our identified co-occurring loss-gain events and theirs (Fisher exact test, Odds ratio (OR) = 15.0, P = 1.65e-39, Methods ).…”

Section: Resultssupporting

confidence: 93%

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Chromosome 7 to the rescue: overcoming chromosome 10 loss in gliomas

Nair,

Schäffer,

Gertz

et al. 2024

Preprint

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The co-occurrence of chromosome 10 loss and chromosome 7 gain in gliomas is the most frequent loss-gain co-aneuploidy pair in human cancers, a phenomenon that has been investigated without resolution since the late 1980s. Expanding beyond previous gene-centric studies, we investigate the co-occurrence in a genome-wide manner taking an evolutionary perspective. First, by mining large tumor aneuploidy data, we predict that the more likely order is 10 loss followed by 7 gain. Second, by analyzing extensive genomic and transcriptomic data from both patients and cell lines, we find that this co-occurrence can be explained by functional rescue interactions that are highly enriched on 7, which can possibly compensate for any detrimental consequences arising from the loss of 10. Finally, by analyzing transcriptomic data from normal, non-cancerous, human brain tissues, we provide a plausible reason why this co-occurrence happens preferentially in cancers originating in certain regions of the brain.

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Section: Resultssupporting

confidence: 93%

“…We compared our results to loss/gain pairs in Supplementary Table 4 in Prasad et al 65,66 . We consider only loss/gain pairs, and therefore take the cancer specific pairs and p-values from Prasad et al, restrict them to the 22 TCGA cancer types we were able to identify, and recompute the FDR correction based on the pairs retained.…”

Section: Methodsmentioning

confidence: 99%