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Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer

Wigard P Kloosterman1, Marlous Hoogstraat12, Oscar Paling2, Masoumeh Tavakoli-Yaraki1, Ivo Renkens1, Joost S Vermaat2, Markus J van Roosmalen1, Stef van Lieshout12, Isaac J Nijman3, Wijnand Roessingh2, Ruben van 't Slot1, José van de Belt1, Victor Guryev3, Marco Koudijs2, Emile Voest2 and Edwin Cuppen13*

Author affiliations

1 Department of Medical Genetics, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands

2 Department of Medical Oncology, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, 3584 CG, The Netherlands

3 Hubrecht Institute KNAW and University Medical Center Utrecht, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands

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Citation and License

Genome Biology 2011, 12:R103  doi:10.1186/gb-2011-12-10-r103

Published: 19 October 2011

Abstract

Background

Structural rearrangements form a major class of somatic variation in cancer genomes. Local chromosome shattering, termed chromothripsis, is a mechanism proposed to be the cause of clustered chromosomal rearrangements and was recently described to occur in a small percentage of tumors. The significance of these clusters for tumor development or metastatic spread is largely unclear.

Results

We used genome-wide long mate-pair sequencing and SNP array profiling to reveal that chromothripsis is a widespread phenomenon in primary colorectal cancer and metastases. We find large and small chromothripsis events in nearly every colorectal tumor sample and show that several breakpoints of chromothripsis clusters and isolated rearrangements affect cancer genes, including NOTCH2, EXO1 and MLL3. We complemented the structural variation studies by sequencing the coding regions of a cancer exome in all colorectal tumor samples and found somatic mutations in 24 genes, including APC, KRAS, SMAD4 and PIK3CA. A pairwise comparison of somatic variations in primary and metastatic samples indicated that many chromothripsis clusters, isolated rearrangements and point mutations are exclusively present in either the primary tumor or the metastasis and may affect cancer genes in a lesion-specific manner.

Conclusions

We conclude that chromothripsis is a prevalent mechanism driving structural rearrangements in colorectal cancer and show that a complex interplay between point mutations, simple copy number changes and chromothripsis events drive colorectal tumor development and metastasis.