Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs

Kevin Hadi; Xiaotong Yao; Julie M. Behr; Aditya Deshpande; Charalampos Xanthopoulakis; Huasong Tian; Sarah Kudman; Joel Rosiene; Madison Darmofal; Joseph DeRose; Rick Mortensen; Emily M. Adney; Alon Shaiber; Zoran Gajic; Michael Sigouros; Kenneth Eng; Jeremiah A. Wala; Kazimierz O. Wrzeszczyński; Kanika Arora; Minita Shah; Anne Katrin Emde; Vanessa Felice; Mayu O. Frank; Robert B. Darnell; Mahmoud Ghandi; Franklin Huang; Sally Dewhurst; John Maciejowski; Titia de Lange; Jeremy Setton; Nadeem Riaz; Jorge S. Reis-Filho; Simon Powell; David A. Knowles; Ed Reznik; Bud Mishra; Rameen Beroukhim; Michael C. Zody; Nicolas Robine; Kenji M. Oman; Carissa A. Sanchez; Mary K. Kuhner; Lucian P. Smith; Patricia C. Galipeau; Thomas G. Paulson; Brian J. Reid; Xiaohong Li; David Wilkes; Andrea Sboner; Juan Miguel Mosquera; Olivier Elemento; Marcin Imielinski

doi:10.1016/j.cell.2020.08.006

Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs

Kevin Hadi, Xiaotong Yao, Julie M. Behr, Aditya Deshpande, Charalampos Xanthopoulakis, Huasong Tian, Sarah Kudman, Joel Rosiene, Madison Darmofal, Joseph DeRose, Rick Mortensen, Emily M. Adney, Alon Shaiber, Zoran Gajic, Michael Sigouros, Kenneth Eng, Jeremiah A. Wala, Kazimierz O. Wrzeszczyński, Kanika Arora, Minita ShahAnne Katrin Emde, Vanessa Felice, Mayu O. Frank, Robert B. Darnell, Mahmoud Ghandi, Franklin Huang, Sally Dewhurst, John Maciejowski, Titia de Lange, Jeremy Setton, Nadeem Riaz, Jorge S. Reis-Filho, Simon Powell, David A. Knowles, Ed Reznik, Bud Mishra, Rameen Beroukhim, Michael C. Zody, Nicolas Robine, Kenji M. Oman, Carissa A. Sanchez, Mary K. Kuhner, Lucian P. Smith, Patricia C. Galipeau, Thomas G. Paulson, Brian J. Reid, Xiaohong Li, David Wilkes, Andrea Sboner, Juan Miguel Mosquera, Olivier Elemento, Marcin Imielinski

Computer Science

Research output: Contribution to journal › Article › peer-review

Abstract

A novel computational approach for inferring and classifying patterns in cancer genome graphs uncovers three classes of complex structural variation with distinct tumor type and genomic distributions.

Original language	English (US)
Pages (from-to)	197-210.e32
Journal	Cell
Volume	183
Issue number	1
DOIs	https://doi.org/10.1016/j.cell.2020.08.006
State	Published - Oct 1 2020

Keywords

aneuploidy
cancer evolution
cancer genomics
chromothripsis
fragile sites
genome graphs
mutational processes
phasing
structural variation
superenhancers

ASJC Scopus subject areas

Biochemistry, Genetics and Molecular Biology(all)

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10.1016/j.cell.2020.08.006

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Hadi, K., Yao, X., Behr, J. M., Deshpande, A., Xanthopoulakis, C., Tian, H., Kudman, S., Rosiene, J., Darmofal, M., DeRose, J., Mortensen, R., Adney, E. M., Shaiber, A., Gajic, Z., Sigouros, M., Eng, K., Wala, J. A., Wrzeszczyński, K. O., Arora, K., ... Imielinski, M. (2020). Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell, 183(1), 197-210.e32. https://doi.org/10.1016/j.cell.2020.08.006

Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. / Hadi, Kevin; Yao, Xiaotong; Behr, Julie M.; Deshpande, Aditya; Xanthopoulakis, Charalampos; Tian, Huasong; Kudman, Sarah; Rosiene, Joel; Darmofal, Madison; DeRose, Joseph; Mortensen, Rick; Adney, Emily M.; Shaiber, Alon; Gajic, Zoran; Sigouros, Michael; Eng, Kenneth; Wala, Jeremiah A.; Wrzeszczyński, Kazimierz O.; Arora, Kanika; Shah, Minita; Emde, Anne Katrin; Felice, Vanessa; Frank, Mayu O.; Darnell, Robert B.; Ghandi, Mahmoud; Huang, Franklin; Dewhurst, Sally; Maciejowski, John; de Lange, Titia; Setton, Jeremy; Riaz, Nadeem; Reis-Filho, Jorge S.; Powell, Simon; Knowles, David A.; Reznik, Ed; Mishra, Bud; Beroukhim, Rameen; Zody, Michael C.; Robine, Nicolas; Oman, Kenji M.; Sanchez, Carissa A.; Kuhner, Mary K.; Smith, Lucian P.; Galipeau, Patricia C.; Paulson, Thomas G.; Reid, Brian J.; Li, Xiaohong; Wilkes, David; Sboner, Andrea; Mosquera, Juan Miguel; Elemento, Olivier; Imielinski, Marcin.

In: Cell, Vol. 183, No. 1, 01.10.2020, p. 197-210.e32.

Research output: Contribution to journal › Article › peer-review

Hadi, K, Yao, X, Behr, JM, Deshpande, A, Xanthopoulakis, C, Tian, H, Kudman, S, Rosiene, J, Darmofal, M, DeRose, J, Mortensen, R, Adney, EM, Shaiber, A, Gajic, Z, Sigouros, M, Eng, K, Wala, JA, Wrzeszczyński, KO, Arora, K, Shah, M, Emde, AK, Felice, V, Frank, MO, Darnell, RB, Ghandi, M, Huang, F, Dewhurst, S, Maciejowski, J, de Lange, T, Setton, J, Riaz, N, Reis-Filho, JS, Powell, S, Knowles, DA, Reznik, E, Mishra, B, Beroukhim, R, Zody, MC, Robine, N, Oman, KM, Sanchez, CA, Kuhner, MK, Smith, LP, Galipeau, PC, Paulson, TG, Reid, BJ, Li, X, Wilkes, D, Sboner, A, Mosquera, JM, Elemento, O & Imielinski, M 2020, 'Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs', Cell, vol. 183, no. 1, pp. 197-210.e32. https://doi.org/10.1016/j.cell.2020.08.006

Hadi, Kevin ; Yao, Xiaotong ; Behr, Julie M. ; Deshpande, Aditya ; Xanthopoulakis, Charalampos ; Tian, Huasong ; Kudman, Sarah ; Rosiene, Joel ; Darmofal, Madison ; DeRose, Joseph ; Mortensen, Rick ; Adney, Emily M. ; Shaiber, Alon ; Gajic, Zoran ; Sigouros, Michael ; Eng, Kenneth ; Wala, Jeremiah A. ; Wrzeszczyński, Kazimierz O. ; Arora, Kanika ; Shah, Minita ; Emde, Anne Katrin ; Felice, Vanessa ; Frank, Mayu O. ; Darnell, Robert B. ; Ghandi, Mahmoud ; Huang, Franklin ; Dewhurst, Sally ; Maciejowski, John ; de Lange, Titia ; Setton, Jeremy ; Riaz, Nadeem ; Reis-Filho, Jorge S. ; Powell, Simon ; Knowles, David A. ; Reznik, Ed ; Mishra, Bud ; Beroukhim, Rameen ; Zody, Michael C. ; Robine, Nicolas ; Oman, Kenji M. ; Sanchez, Carissa A. ; Kuhner, Mary K. ; Smith, Lucian P. ; Galipeau, Patricia C. ; Paulson, Thomas G. ; Reid, Brian J. ; Li, Xiaohong ; Wilkes, David ; Sboner, Andrea ; Mosquera, Juan Miguel ; Elemento, Olivier ; Imielinski, Marcin. / Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. In: Cell. 2020 ; Vol. 183, No. 1. pp. 197-210.e32.

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