The subclonal structure and genomic evolution of oral squamous cell carcinoma revealed by ultra-deep sequencing
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Siavosh Tabatabaeifar1,4, Mads Thomassen2,4, Martin J. Larsen2,4, Stine R. Larsen3,4, Torben A. Kruse2,4,*, Jens A. Sørensen1,4,*
1Department of Plastic Surgery, Odense University Hospital, Odense, Denmark
2Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
3Department of Clinical Pathology, Odense University Hospital, Odense, Denmark
4Department of University of Southern Denmark, Institute of Clinical Research, Odense, Denmark
*These authors contributed equally to this work
Siavosh Tabatabaeifar, email: Siavosh.Tabatabaeifar@rsyd.dk
Keywords: ultra-deep sequencing, oral squamous cell carcinoma, tumor heterogeneity, subclonal structure, genomic evolution
Received: September 13, 2016 Accepted: January 24, 2017 Published: February 02, 2017
Recent studies suggest that head and neck squamous cell carcinomas are very heterogeneous between patients; however the subclonal structure remains unexplored mainly due to studies using only a single biopsy per patient. To deconvolute the clonal structure and describe the genomic cancer evolution, we applied whole-exome sequencing combined with ultra-deep targeted sequencing on oral squamous cell carcinomas (OSCC). From each patient, a set of biopsies was sampled from distinct geographical sites in primary tumor and lymph node metastasis.
We demonstrate that the included OSCCs show a high degree of inter-patient heterogeneity but a low degree of intra-tumor heterogeneity. However, some OSCC cancers contain complex subclonal architectures comprising distinct subclones only found in geographically distinct regions of the primary tumors. In several cases we find mutations in the primary tumor that are not present in the lymph node metastasis. We conclude that metastatic potential in our population is acquired early in tumor evolution as evident by the ongoing parallel evolution in several primary tumors.
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