Open Access Open Badges Research article

Intratumoral genetic heterogeneity in metastatic melanoma is accompanied by variation in malignant behaviors

Matthew Anaka12, Christopher Hudson1, Pu-Han Lo1, Hongdo Do34, Otavia L Caballero5, Ian D Davis67, Alexander Dobrovic34, Jonathan Cebon128* and Andreas Behren1

Author Affiliations

1 Cancer Immuno-biology Lab, Ludwig Institute for Cancer Research Melbourne, Austin Branch, Melbourne, Victoria 3084, Australia

2 Department of Medicine, Austin Health, University of Melbourne, Parkville, Victoria 3010, Australia

3 Molecular Pathology Research and Development Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria 3002, Australia

4 Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia

5 Department of Neurosurgery, John Hopkins University School of Medicine, Baltimore, MD 21231, USA

6 Uro-Oncology Lab, Ludwig Institute for Cancer Research Melbourne, Austin Branch, Melbourne, Victoria 3084, Australia

7 Current Address: Monash University and Eastern Health, Box Hill, Victoria 3128, Australia

8 Ludwig Institute For Cancer Research, Level 5, Olivia Newton-John Cancer & Wellness Centre, Studley Road, Heidelberg, Victoria 3084, Australia

For all author emails, please log on.

BMC Medical Genomics 2013, 6:40  doi:10.1186/1755-8794-6-40

Published: 11 October 2013



Intratumoral heterogeneity is a major obstacle for the treatment of cancer, as the presence of even minor populations that are insensitive to therapy can lead to disease relapse. Increased clonal diversity has been correlated with a poor prognosis for cancer patients, and we therefore examined genetic, transcriptional, and functional diversity in metastatic melanoma.


Amplicon sequencing and SNP microarrays were used to profile somatic mutations and DNA copy number changes in multiple regions from metastatic lesions. Clonal genetic and transcriptional heterogeneity was also assessed in single cell clones from early passage cell lines, which were then subjected to clonogenicity and drug sensitivity assays.


MAPK pathway and tumor suppressor mutations were identified in all regions of the melanoma metastases analyzed. In contrast, we identified copy number abnormalities present in only some regions in addition to homogeneously present changes, suggesting ongoing genetic evolution following metastatic spread. Copy number heterogeneity from a tumor was represented in matched cell line clones, which also varied in their clonogenicity and drug sensitivity. Minor clones were identified based on dissimilarity to the parental cell line, and these clones were the most clonogenic and least sensitive to drugs. Finally, treatment of a polyclonal cell line with paclitaxel to enrich for drug-resistant cells resulted in the adoption of a gene expression profile with features of one of the minor clones, supporting the idea that these populations can mediate disease relapse.


Our results support the hypothesis that minor clones might have major consequences for patient outcomes in melanoma.

Melanoma; Microarray; Heterogeneity; Mutation profiling; Copy number; Clonal