Weaver, B. A. & Cleveland, D. W. Does aneuploidy cause cancer? Curr. Opin. Cell Biol. 18, 658–667 (2006).
Taylor, A. M. et al. Genomic and functional approaches to understanding cancer aneuploidy. Cancer Cell 33, 676–689 (2018).
Boveri, T. Concerning the origin of malignant tumours by Theodor Boveri. Translated and annotated by Henry Harris. J. Cell Sci. 121, 1–84 (2008).
Holland, A. J. & Cleveland, D. W. Boveri revisited: chromosomal instability, aneuploidy and tumorigenesis. Nat. Rev. Mol. Cell Biol. 10, 478–487 (2009).
Sheltzer, J. M. et al. Single-chromosome gains commonly function as tumor suppressors. Cancer Cell 31, 240–255 (2017).
Pavelka, N. et al. Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. Nature 468, 321–325 (2010).
Ly, P. et al. Characterization of aneuploid populations with trisomy 7 and 20 derived from diploid human colonic epithelial cells. Neoplasia 13, 348–357 (2011).
Rutledge, S. D. et al. Selective advantage of trisomic human cells cultured in non-standard conditions. Sci. Rep. 6, 22828 (2016).
Sunshine, A. B. et al. The fitness consequences of aneuploidy are driven by condition-dependent gene effects. PLoS Biol. 13, e1002155 (2015).
Ravichandran, M. C., Fink, S., Clarke, M. N., Hofer, F. C. & Campbell, C. S. Genetic interactions between specific chromosome copy number alterations dictate complex aneuploidy patterns. Genes Dev. 32, 1485–1498 (2018).
Hughes, T. R. et al. Widespread aneuploidy revealed by DNA microarray expression profiling. Nat. Genet. 25, 333–337 (2000).
Liu, G. et al. Gene essentiality is a quantitative property linked to cellular evolvability. Cell 163, 1388–1399 (2015).
Salehi, S. et al. Clonal fitness inferred from time-series modelling of single-cell cancer genomes. Nature 595, 585–590 (2021).
Kimmel, G. J. et al. Intra-tumor heterogeneity, turnover rate and karyotype space shape susceptibility to missegregation-induced extinction. PLoS Comput. Biol. 19, e1010815 (2023).
Lee, A. J. X. et al. Chromosomal instability confers intrinsic multidrug resistance. Cancer Res. 71, 1858–1870 (2011).
Cai, Y. et al. Loss of chromosome 8p governs tumor progression and drug response by altering lipid metabolism. Cancer Cell 29, 751–766 (2016).
Uno, N. et al. CRISPR/Cas9-induced transgene insertion and telomere-associated truncation of a single human chromosome for chromosome engineering in CHO and A9 cells. Sci. Rep. 7, 12739 (2017).
Mermel, C. H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
Brennan, C. W. et al. The somatic genomic landscape of glioblastoma. Cell 155, 462–477 (2013).
Cimini, D. Merotelic kinetochore orientation, aneuploidy, and cancer. Biochim. Biophys. Acta 1786, 32–40 (2008).
Blackford, A. N. & Stucki, M. How cells respond to DNA breaks in mitosis. Trends Biochem. Sci. 45, 321–331 (2020).
Martincorena, I. et al. Universal patterns of selection in cancer and somatic tissues. Cell 171, 1029–1041 (2017).
Hoadley, K. A. et al. Cell-of-origin patterns dominate the molecular classification of 10,000 tumors from 33 types of cancer. Cell 173, 291–304 (2018).
Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899–905 (2010).
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020).
Xue, W. et al. A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions. Proc. Natl Acad. Sci. USA 109, 8212–8217 (2012).
Chan, E. M. et al. WRN helicase is a synthetic lethal target in microsatellite unstable cancers. Nature 568, 551–556 (2019).
Bailey, M. H. et al. Comprehensive characterization of cancer driver genes and mutations. Cell 173, 371–385 (2018).
Ciriello, G. et al. Emerging landscape of oncogenic signatures across human cancers. Nat. Genet. 45, 1127–1133 (2013).
Nichols, C. A. et al. Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities. Nat. Commun. 11, 2517 (2020).
McFarland, J. M. et al. Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nat. Commun. 9, 4610 (2018).
Dempster, J. M. et al. Chronos: a cell population dynamics model of CRISPR experiments that improves inference of gene fitness effects. Genome Biol. 22, 343 (2021).
Davoli, T. et al. Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell 155, 948–962 (2013).
Dewhurst, S. M. et al. Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution. Cancer Discov. 4, 175–185 (2014).
López, S. et al. Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution. Nat. Genet. 52, 283–293 (2020).
Zack, T. I. et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45, 1134–1140 (2013).
Liu, Y. et al. Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells. Nat. Commun. 8, 1212 (2017).
Hose, J. et al. Dosage compensation can buffer copy-number variation in wild yeast. Elife 4, e05462 (2015).
Stenberg, P. et al. Buffering of segmental and chromosomal aneuploidies in Drosophila melanogaster. PLoS Genet. 5, e1000465 (2009).
Muenzner, J. et al. The natural diversity of the yeast proteome reveals chromosome-wide dosage compensation in aneuploids. Preprint at bioRxiv https://doi.org/10.1101/2022.04.06.487392 (2022).
Dumont, M. et al. Human chromosome-specific aneuploidy is influenced by DNA-dependent centromeric features. EMBO J. 39, e102924 (2020).
Klaasen, S. J. et al. Nuclear chromosome locations dictate segregation error frequencies. Nature 607, 604–609 (2022).
Bersani, F. et al. Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer. Proc. Natl Acad. Sci. USA 112, 15148–15153 (2015).
Quinodoz, S. A. et al. Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus. Cell 174, 744–757 (2018).
Kitagawa, K. & Hieter, P. Evolutionary conservation between budding yeast and human kinetochores. Nat. Rev. Mol. Cell Biol. 2, 678–687 (2001).
Barra, V. & Fachinetti, D. The dark side of centromeres: types, causes and consequences of structural abnormalities implicating centromeric DNA. Nat. Commun. 9, 4340 (2018).
Knutsen, T. et al. Definitive molecular cytogenetic characterization of 15 colorectal cancer cell lines. Genes Chromosomes Cancer 49, 204–223 (2010).
Nurk, S. et al. The complete sequence of a human genome. Science 376, 44–53 (2022).
Altemose, N. et al. Complete genomic and epigenetic maps of human centromeres. Science 376, eabl4178 (2022).
Gregan, J., Polakova, S., Zhang, L., Tolić-Nørrelykke, I. M. & Cimini, D. Merotelic kinetochore attachment: causes and effects. Trends Cell Biol. 21, 374–381 (2011).
Gisselsson, D. et al. Telomere dysfunction triggers extensive DNA fragmentation and evolution of complex chromosome abnormalities in human malignant tumors. Proc. Natl Acad. Sci. USA 98, 12683–12688 (2001).
Wise, J. L. et al. Human telomere length correlates to the size of the associated chromosome arm. PLoS ONE 4, e6013 (2009).
McCarroll, S. A. et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet. 40, 1166–1174 (2008).
Korn, J. M. et al. Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs. Nat. Genet. 40, 1253–1260 (2008).
Cancer Genome Atlas Research, Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609–615 (2011).
Gao, G. F. et al. Tangent normalization for somatic copy-number inference in cancer genome analysis. Bioinformatics 38, 4677–4686 (2022).
Olshen, A. B., Venkatraman, E. S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557–572 (2004).
Carter, S. L. et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30, 413–421 (2012).
Li, Y. et al. Patterns of somatic structural variation in human cancer genomes. Nature 578, 112–121 (2020).
Gao, Q. et al. Driver fusions and their implications in the development and treatment of human cancers. Cell Rep. 23, 227–238 (2018).
Saghafinia, S., Mina, M., Riggi, N., Hanahan, D. & Ciriello, G. Pan-cancer landscape of aberrant DNA methylation across human tumors. Cell Rep. 25, 1066–1080 (2018).
Delignette-Muller, M. L. & Dutang, C. fitdistrplus: An R package for fitting distributions. J. Stat. Softw. 64, 1–34 (2015).
Benjamini, Y. & Yekutieli, D. The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 29, 1165–1188 (2001).
Miotto, B., Ji, Z. & Struhl, K. Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers. Proc. Natl Acad. Sci. USA 113, E4810–E4819 (2016).
Sondka, Z. et al. The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers. Nat. Rev. Cancer 18, 696–705 (2018).
Endres, D. M. & Schindelin, J. E. A new metric for probability distributions. IEEE Trans. Inf. Theory 49, 1858–1860 (2003).
Lin, J. Divergence measures based on the Shannon entropy. IEEE Trans. Inf. Theory 37, 145–151 (1991).
Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9, e1003118 (2013).
Gel, B. et al. regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests. Bioinformatics 32, 289–291 (2016).
Kim, S. Y., Jacob, L. & Speed, T. P. Combining calls from multiple somatic mutation-callers. BMC Bioinform. 15, 154 (2014).
Kasar, S. et al. Whole-genome sequencing reveals activation-induced cytidine deaminase signatures during indolent chronic lymphocytic leukaemia evolution. Nat. Commun. 6, 8866 (2015).
Kim, J. et al. Somatic ERCC2 mutations are associated with a distinct genomic signature in urothelial tumors. Nat. Genet. 48, 600–606 (2016).
Knijnenburg, T. A. et al. Genomic and molecular landscape of DNA damage repair deficiency across The Cancer Genome Atlas. Cell Rep. 23, 239–254 (2018).
Lundberg, A. S. et al. Immortalization and transformation of primary human airway epithelial cells by gene transfer. Oncogene 21, 4577–4586 (2002).
Adalsteinsson, V. A. et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat. Commun. 8, 1324 (2017).
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).
Van der Auwera, G. & O’Connor, B. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra (O’Reilly Media, 2020).
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