Recent technological advancements in the genomics field contribute to cancer research substantially. Next generation sequencing (NGS) and microarray technologies have become widely used by many scientists to analyse biology of cancer cells and detect mutations that can explain cancer predisposition. With the information that these technologies provide, physicians have the opportunity or means to make diagnosis of diseases more accurately and choose better treatment plans for their patients.
Cancer causing mutations can be analysed in two categories: germline mutations and somatic mutations.
Germline mutations, which are observed in germ cells, can cause individuals to be prone to develop certain cancer types. These mutations can be identified using different methods. One such method uses next generation sequencing technology to sequence whole genome of an individual, another method uses microarray technology to perform GWAS. Apart from these methods, a targeted sequencing method can also be preferred. While whole genome sequencing provides information about all germline mutations observed within the cancer genome, with targeted sequencing the scientists have the opportunity to focus on the genes that are known to play an important role in cancer predisposition and analyse only the mutations that are observed on those genes.
Somatic mutations are the mutations that are observed in any cell except the germ cells. In order to detect somatic mutations, a whole genome sequencing can be performed. As it is the case with germline mutations, while whole genome sequencing provides information about all somatic mutations observed within the cancer genome, with targeted sequencing the scientists have the opportunity to focus on a subset of genes and analyse only the mutations that are observed on those genes. Another approach that is used in somatic mutation detection is whole exon sequencing. This approach focuses only on exon sites (protein coding DNA segments) that are known to contain cancer causing somatic mutations.
Epigenetic changes (abnormal metilation, changes in transcription factor binding, etc.) are frequently observed in the cells of cancer patients. By affecting gene expression, these epigenetic changes can be used to detect important tumor development pathways. Therefore, identification of epigenetic changes is important in monitoring the development and progression of cancer. It should be noted that detection of the changes in the transcriptome is also equally important in understanding tumor development.
Chromosomal anomaly studies provide in depth information about cancer etiology and development. There are certain types of chromosomal anomalies that are frequently observed in cancer cells; such as gene fusions, chromosomal rearrangements, copy number variants. With the help of advanced sequencing and microarray technologies, it is now much more easier to detect such anomalies.