Tumor DNA Analysis in the Tissue

In recent years, high-throughput systems have increasingly been developed which enable the simultaneous sequencing of millions of individual DNA fragments (next-generation sequencing). We routinely use the Ion AmpliSeq™Cancer Hotspot Panel v2 in collaboration with the medical care center laboratory of Dr. Fenner and colleagues. It allows DNA fragment libraries from the genomic “hot spot” regions, which are frequently mutated in human cancer genes, to be produced from very small amounts of DNA from a single primer pool using multiplex PCR. These “hot spot” regions include ~2800 COSMIC mutations of 50 oncogenes and tumor suppressor genes, in which the genes KRAS, BRAF, and EGFR are comprehensively covered. The benefits of NGS include the small DNA amounts of about 10 ng per DNA sample to be used and the possibility of analyzing cryopreserved and also formalin-fixed tissue samples.