Oncogene amplification is a critical driver of cancer. Cytogenetic characterization on FFPE samples is a cost-effective way to study oncogene amplification. We present robust and comprehensive instructions for investigating focal gene amplification and FFPE samples.
By examining the FISH signal pattern, it becomes unequivocally clear whether and how a gene locus is amplified. Oncogenes amplified as extra chromosomal DNA are found to be prevalent in human cancer, such as lung, breast, and brain cancer. Whole genome sequencing and FISH are the most widely used methods to detect extrachromosomal DNA.
Applying FISH to FFPE tissues is challenging because cross-linking artifacts and background autofluorescence often undermine data quality. Our protocol includes optimized procedures, including protein extraction and digestion, heat-denaturing, and autofluorescence quenching techniques to improve data quality during FISH on FFPE samples, which will give valuable insight into cancer progression in patients. We will study the molecular functions of extrachromosomal DNA, and how cancer cells maintain extrachromosomal DNA.
Ultimately, we aim to eliminate them to treat cancer.
