Exploring the landscape of focal amplifications in cancer using AmpliconArchitect

Nature Communications, Journal Year: 2019, Volume and Issue: 10(1)

Published: Jan. 23, 2019

Abstract Focal oncogene amplification and rearrangements drive tumor growth evolution in multiple cancer types. We present AmpliconArchitect (AA), a tool to reconstruct the fine structure of focally amplified regions using whole genome sequencing (WGS) validate it extensively on simulated real datasets, across wide range coverage copy numbers. Analysis AA-reconstructed amplicons pan-cancer dataset reveals many novel properties number amplifications cancer. These findings support model which focal arise due formation replication extrachromosomal DNA. Applying AA 68 viral-mediated samples, we identify large fraction with specific structural signatures suggestive hybrid, human-viral reconstruction, integrated metaphase fluorescence situ hybridization (FISH) PacBio cell-line UPCI:SCC090 confirm origin Forkhead box E1 ( FOXE1 )-containing hybrid amplicon.

Language: Английский

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The impact of mitotic errors on cell proliferation and tumorigenesis

Genes & Development, Journal Year: 2018, Volume and Issue: 32(9-10), P. 620 - 638

Published: May 1, 2018

Mitosis is a delicate event that must be executed with high fidelity to ensure genomic stability. Recent work has provided insight into how mitotic errors shape cancer genomes by driving both numerical and structural alterations in chromosomes contribute tumor initiation progression. Here, we review the sources of human tumors their effect on cell fitness transformation. We discuss new findings suggest chromosome missegregation can produce proinflammatory environment impact responsiveness immunotherapy. Finally, survey vulnerabilities exposed division they exploited therapeutically.

Language: Английский

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Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells

Trends in Genetics, Journal Year: 2018, Volume and Issue: 34(4), P. 270 - 278

Published: Jan. 9, 2018

Language: Английский

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Tracing Oncogene Rearrangements in the Mutational History of Lung Adenocarcinoma

Cell, Journal Year: 2019, Volume and Issue: 177(7), P. 1842 - 1857.e21

Published: May 30, 2019

Language: Английский

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ecDNA hubs drive cooperative intermolecular oncogene expression

Nature, Journal Year: 2021, Volume and Issue: 600(7890), P. 731 - 736

Published: Nov. 24, 2021

Language: Английский

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