Question: Does Cell Ranger DNA provide information about mitochondrial DNA?
Answer: The Chromium Single Cell DNA workflow does capture mitochondrial DNA from encapsulated cells, however the Single Cell CNV Solution does not perform copy number variant analysis reads derived from the mitochondrial genome.
There are a few reasons why:
- Copy number calling is relative. It is based on the assumption that the entire genome from an individual cell is represented proportionally by the reads that are captured. Since we don't know how many copies of the mitochondrial genome may have been captured from a given cell, there is no way to relate those read counts to those from the nuclear genome. This would not be necessary if we explicitly treated the mitochondrial genome as independent from the nuclear genome, however at this time we do not do that.
- The properties of the small circular mitochondrial genome in the assay may be different from long linear genomic DNA fragments, including amplification efficiency and retention in the cell beads.
- The small size of the mitochondrial genome (16 kb) is smaller than the bin size used in by the CNV detection algorithm (20 kb).