Different Genome Changes Observed in Cancer Cells
(also http://shapiro.bsd.uchicago.edu/Cancer%20Genome%20Changes.pdf)

Genome Change


Stress-induced mutagenic activity

(Cisneros, Bussey et al. 2017)

Hypermutability following loss of replication proofreading functions

(Shlien, Campbell et al. 2015)

Massive genome rearrangements (“karyotype chaos”)

(Stephens, Greenman et al. 2011; Nones, Waddell et al. 2014; Rangel, Forero-Castro et al. 2017)

Homology-independent rearrangements (NHEJ)

(Malhotra, Lindberg et al. 2013)

Retrotransposon activation

(Anwar, Wulaningsih et al. 2017)

Non-canonical termination of homologous recombination

(Hartlerode, Willis et al. 2016)

Kataegis ("mutation thunderstorms") and somatic hypermutation

(Hardianti, Tatsumi et al. 2004; Nik-Zainal, Alexandrov et al. 2012; Nik-Zainal, Van Loo et al. 2012; Stephens, Tarpey et al. 2012; Chan, Roberts et al. 2015; Harris 2015; Kazanov, Roberts et al. 2015; Supek and Lehner 2017)

Cytosine deaminase-dependent chromosome translocation

(Robbiani and Nussenzweig 2013; Harris 2015; Kazanov, Roberts et al. 2015)

Chromothripsis ("chromosome shattering")

(Kloosterman, Hoogstraat et al. 2011; Cai, Kumar et al. 2014; Kloosterman, Koster et al. 2014; de Pagter and Kloosterman 2015; Rode, Maass et al. 2016)

Chromothripsis linked to oncogene amplification

(Furgason, Koncar et al. 2015)

Complex insertion-deletion mutations (indels)

(Ye, Wang et al. 2015)

Tandem duplications as well as formation of “amplicons” with rearranged and amplified chromosomal segments, a.k.a. copy number variations (CNVs)

(Beroukhim, Mermel et al. 2010; Inaki, Menghi et al. 2014; Menghi, Inaki et al. 2016)

Formation of amplified circular extrachromosomal DNAs

(Turner, Deshpande et al. 2017)

Processed pseudogene formation

(Cooke, Shlien et al. 2014)

L1 retrotransposition

(Lee, Iskow et al. 2012; Helman, Lawrence et al. 2014; Kemp and Longworth 2015; Scott and Devine 2017)

Extensive L1 retrotransduction of non-repetitive DNA

(Tubio, Li et al. 2014)

Transfer of mitochondrial DNA into nuclear genome

(Ju, Tubio et al. 2015)

RAG transposase/recombinase-mediated chromosome rearrangement in immune system tumors

(Halper-Stromberg, Steranka et al. 2013; Papaemmanuil, Rapado et al. 2014)

Somatic hypermutation involving a reverse transcriptase-based mutator activity

(Steele 2016)





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