Targeted resequencing can be employed to identify genetic variants in a selected subset of genes. The target enrichment is typically achieved using amplicon- or hybridization-based approaches and is chosen depending on the research project. Common applications of targeted resequencing include:
Deconvolution of genetic screens
In the last years, genetic screens using pooled lentiviral shRNA or sgRNA libraries have been successfully employed to decipher diverse oncogenic mechanisms. HTS is typically used to compare the representation of the targeting constructs in different conditions or cell pools.
DNA methylation regulates gene expression and is involved in the development of cancer. Chip-based whole-genome methylation analysis can help to access methylation patterns at the genome or gene level. Methylation analysis in the core unit is performed using the Illumina Infinium MethylationEPIC BeadChip on the Illumina IScan platform. Apart from the DNA methylation analysis, this technique also allows determination of copy number profiles.
Illustration of hierarchical cluster analysis of differentially methylated CpGs in different brain tumor entities including principal component analysis of the same specimen: