Next-generation sequencing (NGS) technologies are adding new evidence for genetic diversity both within and between common tumours. NGS methodologies comprehensively and systematically determine both nucleotide sequence and copy number of genomic loci, and have the advantage of being able to simultaneously sequence heterogeneous mixtures of genomes in a given sample, which might include tumour, stromal, and immune cells.
Both NGS and comparative genomic hybridisation studies in breast cancer suggest marked genetic intra-tumour heterogeneity (Torres et al, 2007
; Shah et al, 2009
; Navin et al, 2010
). In particular, Navin et al (2010)
demonstrated the existence of subclones that were derived from a common clonal progenitor, which varied between samples taken from different regions of the same primary tumour as well as subclones with distinct patterns of DNA copy number variation within the same sector of tumour. In these polygenomic tumours, subpopulation of cells could be anatomically separate or intermixed. There was no correlation between different tumour grades or immunohistochemical staining patterns and genomic heterogeneity.
Intratumour heterogeneity in glioblastoma heterogeneity in glioblastoma is also apparent (Snuderl et al, 2011
; Nickel et al, 2012
; Szerlip et al, 2012
). One study identified intermingled population of cells with mutually exclusive amplifications of different receptor tyrosine kinases (RTKs) such as PDGFRA, MET, and EGFR, with subpopulation sharing similar alterations in CDKN2A
genes, consistent with a single common ancestral precursor (Snuderl et al, 2011
). A second study confirmed intra-tumour heterogeneity of amplification of RTKs in glioblastoma and demonstrated that such heterogeneity results in functionally distinct and reduced sensitivity to targeted therapeutics (Szerlip et al, 2012
). Spatial and temporal heterogeneity was characterised by targeted NGS in seven primary and recurrent tumour samples from one patient with glioblastoma; in this study, the variant allelic frequency of somatic mutations in EGFR, PI3KCA, PTEN, and TP53 vs
wild type varied between focal regions of the same tumour, and between the time points of diagnosis, first recurrence and second recurrence (Nickel et al, 2012
Spatial genomic heterogeneity has been recently documented in renal cell carcinoma (RCC) raising the potential for tumour sampling bias to confound biomarker interpretation (Gerlinger et al, 2012
). Exome sequencing of multiple tumour samples from primary and metastatic lesions in two patients with clear cell RCC revealed extensive intra-tumour heterogeneity, which was demonstrated in genetic and transcriptomic analyses. Distinct loss of function somatic events in multiple tumour suppressor genes occurred in spatially separated regions of the same tumour, demonstrating convergent evolution and potentially predictable routes to tumour progression. Approximately 30–35% of mutations were shared between regions taken from multiple sites of the primary and metastases. Supporting evidence for intratumour heterogeneity in clear cell RCC, single cell exome sequencing of a clear cell RCC confirmed a complex genomic landscape, with a small number of genes mutated in a large proportion of cells and a greater number of genes mutated at low frequency (Xu et al, 2012
Importantly, some of the earlier studies based on Sanger sequencing or low depth NGS may underestimate the degree of genomic heterogeneity due to limitations of sequencing depth that preclude the identification of rarer tumour subpopulations, and the study by Xu et al
suggests that single cell approaches may be required to assay rare subclones. Furthermore, aberrations mediated through post-translational and epigenetic modifications as well as stochastic and unpredictable behavioural diversity of subclones with similar genotypic identities (Kreso et al, 2012
) are likely to complicate the picture of intratumour heterogeneity further.