Transcript detection and cancer genomics Flashcards
What are driver- and passenger mutations?
Driver mutations: Progress cancer directly. Occurs in proto-oncogenes or tumor suppressor genes (TSGs).
- Proto-oncogenes regulate the cell cycle.
- TSGs suppressor genes normally halt the cell cycle.
Passenger mutations: Random mutagenesis in the genome leading to adverse effects.
Why is the cancer transcriptome interesting?
- By assaying the cancer transcriptome, we get an understanding of which mutations have occurred and whether they have the potential to cause loss-of-function mutation or simply modulate the functions.
A genetic deletion in a promoter region may deactivate an entire locus, these genes won’t show up in the transcriptomic analysis.
- We can look for tissue-specific cancer characteristics.
When performing RNAseq w/ any NGS you can design your sequencing as a balanced block design or a confounded design. What does this mean?
When sequencing multiple RNA samples you can choose one of the aforementioned methods.
Confounded block design: One sample per sequencing. Since biological and technical errors cannot be controlled for, the data becomes less trustworthy. A deviant measurement due to faulty equipment may have caused a significant measurement, or the biological sample was indeed significantly different.
Balanced block design: RNA from the various samples are mixed before analysis, and each sequencing will contain equal parts of each RNA sample. If the sequencing fails, it will be systemically throughout all samples. If one of the samples fails, it will be visible in the quantification.
What are the benefits of generating pair-end repeats vs single-end repeats?
Pair end repeats have adapters ligated at both ends. The entire sequence will not be sequenced, but the ends will. When sequencing this way you can align repetitive regions more easily and the sequencing takes half the time as it’s done from two directions.
