Mutational heterogeneity between different regional tumour grades of clear cell renal cell carcinoma

Only a limited number of studies have explored the possible associations between tumour grade and mutated
genes in clear cell renal cell carcinoma (ccRCC), and we set out to investigate this further using a multiple
sampling and next generation sequencing (NGS) approach in a series of ccRCCs. Multiple regions were sampled
from formalin-fixated paraffin-embedded ccRCC tumour blocks from seven patients. In 27 samples from six
patients, we performed targeted NGS using a custom 42-gene panel based on the most frequently mutated genes
in ccRCC reported in public databases. In four samples from the seventh patient, we performed whole exome
sequencing (WES) and array comparative genomic hybridisation for detection of copy number variants (CNVs).
Mutated genes and the tumour grades of the samples in which they had been identified were compared both
within and between all individual tumours. CNVs were compared across all samples from patient 7. We identified
clear genetic heterogeneity within and across tumours, but VHL mutations were seen in all patients.
Looking across all samples, we identified eleven genes that were only mutated in samples with one particular
tumour grade. However, these genes were never mutated in all samples with that tumour grade. Increasing
chromosomal instability corresponded with increasing tumour grade, but we observed minimal association
between tumour grade and total mutational load in the WES data. Our study confirms the genetic heterogeneity
and tumour grade heterogeneity of ccRCC. Although a relatively small number of samples was analysed, genes
were identified that could potentially be specific, though insensitive, markers of higher ccRCC tumour grades.