Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes
By
Stefan Dentro,
Ignaty Leshchiner,
Kerstin Haase,
Maxime Tarabichi,
Jeff A. Wintersinger,
Amit G. Deshwar,
Kaixian Yu,
Yulia Rubanova,
Geoff Macintyre,
Jonas Demeulemeester,
Ignacio Vázquez-García,
Kortine Kleinheinz,
Dimitri G Livitz,
Salem Malikic,
Nilgun Donmez,
Subhajit Sengupta,
Pavana Anur,
Clemency Jolly,
Marek Cmero,
Daniel Rosebrock,
Steven Schumacher,
Yu Fan,
Matthew W Fittall,
Ruben M. Drews,
Xiaotong Yao,
Juhee Lee,
Matthias Schlesner,
Hongtu Zhu,
David J. Adams,
Gad Getz,
Paul C Boutros,
Marcin Imielinski,
Rameen Beroukhim,
S. Cenk Sahinalp,
Yuan Ji,
Martin Peifer,
Inigo Martincorena,
Florian Markowetz,
Ville Mustonen,
Ke Yuan,
Moritz Gerstung,
Paul T Spellman,
Wenyi Wang,
Quaid Morris,
David C Wedge,
Peter Van Loo,
on behalf of the PCAWG Evolution and Heterogeneity Working Groupthe PCAWG consortium.,
the PCAWG consortium
Posted 05 May 2018
bioRxiv DOI: 10.1101/312041
Intra-tumor heterogeneity (ITH) is a mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin and drivers of ITH across cancer types are poorly understood. To address this question, we extensively characterize ITH across whole-genome sequences of 2,658 cancer samples, spanning 38 cancer types. Nearly all informative samples (95.1%) contain evidence of distinct subclonal expansions, with frequent branching relationships between subclones. We observe positive selection of subclonal driver mutations across most cancer types, and identify cancer type specific subclonal patterns of driver gene mutations, fusions, structural variants and copy-number alterations, as well as dynamic changes in mutational processes between subclonal expansions. Our results underline the importance of ITH and its drivers in tumor evolution, and provide an unprecedented pan-cancer resource of comprehensively annotated subclonal events from whole-genome sequencing data. ### Competing Interest Statement R.B. owns equity in Ampressa Therapeutics. G.G. receives research funds from IBM and Pharmacyclics and is an inventor on patent applications related to MuTect, ABSOLUTE, MutSig, MSMuTect and POLYSOLVER. I.L. is a consultant for PACT Pharma. B.J.R. is a consultant at and has ownership interest (including stock and patents) in Medley Genomics. All other authors declare no competing interests.
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