weshorton
commented
7 years ago - Turn to milestone
- Relevant issues/ create new issues
- Issue 1 - primer competition b/w spikes and gDNA (in PCR) - update this issue to look at both sides, not just spike results, but DNA results as well.
- new issue - read competition b/w spikes and DNA (in sequencing) - standalone
Summary
The amount of T-cells within a sample is variable. T-cells commonly comprise ~15% of total cells in blood samples, but can range anywhere from 0-15% of total cells in tumor samples. Using a standard spike concentration for all samples will cause some of the tumor samples to have most reads comprised of spike DNA. How will this affect depth and breadth of coverage for those samples?
Significance
We need to know if rare clonotypes will be omitted from samples with high percentages of spiked reads. In addition, we must be able to compare among samples with differing abundances of spiked reads. If high levels of spikes depress the clonotype counts of that sample, clonotypes shared between other samples will be artificially lower when compared.
To Do
Potential control experiment: use the same initial T-cell DNA, add variable amounts of spikes, and compare final counts. Will this be able to be determined by the control experiment in Issue #5?
Relevant Information
Results of experiment from issue #5, potentially other experiment.