I have been told that different providers have different gene sets designed for their exome enrichment kits. What are good examples of exome enrichment kits that will cover the genic regions in the mitochondrial genome?
EDIT: I am interested in looking at the mitochondrial data in publicly available exome sequencing datasets, and would like to prioritize for those that are supposed to have good coverage over the mitochondrial genes.
EDIT2: So far, I got the following:
Agilent SureSelect does not specifically target mitochondrial genes, and gives a background coverage of 5-20x.
I mainly work with Agilent SureSelect and it does not specifically target mitochondrial DNA, however we do see it in some samples. It's low coverage however - 5-20x over most of the mitochondrial genome. Probably not suitable for your application. Most exome capture methods will have a list of the baits and targets, so you should just survey them to see which ones specifically include baits for it. I'm not aware of any off the top of my head.
just to say that we've seen this too in our exome captures, but since it isn't systematic across all samples sequenced we couldn't decide to implement anything regarding mtDNA in our default pipeline. something that, by the way, would definitely help to assess the sequencing quality.
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It sounds like you are just interested in the mitochondrial genome. If that is the case, then why not do a mitochondrial DNA prep? If you are asking about something else like mitochondrial genes in the nuclear genome, please clarify.
EDIT: if I look at publicly available exome sequencing datasets, what kind of mitochondrial gene coverage am I expected to obtain?
If I were doing this, I would look for a targeted capture of the mitochondrial genome, and aim for very deep coverage to account for heteroplasmy. Think of this the same way as approaching mosaicism -- the more x coverage the better to detect all variants. I would not rely on traditional depth of coverage (ie around 100x or so) that most labs aim for with exome seq. Also, plan on sequencing multiple different tissues -- as it is known there can be considerable variation in mt genome from tissue to tissue. Just my $0.05
I don't know of very many publicly available targeted capture datasets of the mitochondrial genome. Hence my question about exome: it's more commonly available.
As an aside I don't think 100x is 'traditional' coverage for an exome. 50x is much more routine.