can delly identify multiple copies of a unique deletion?

Question

[Assa Yeroslaviz]

Let's say we have the following situation.

We have a unique breakpoint in mtDNA (a deletion in the mtDNA). If by chance this molecule is replicated and now this unique molecule exist as multiple copies.

How would delly handle this situation? Can it distungish how many molecules exits in the sample? if by counting this unique breakpoint only once with the software, is it be possible that we are not considering the abundance of this unique breakpoint.

I would appreciate any hints also as to where I can look it up.

thanks

Assa

Answer 1

[Vitis]

Considering inheritance of MtDNA as haplotypes, wouldn't any heterozygosity of the deletion detected indicate some sort of mosaicism, i. e. cells containing both MtDNAs with and without the deletion?

Quantifying them is a whole different problem since there probably are PCR amplifications involved in library preparation before sequencing. One approach to take care of that is to use ThruPLEX tag-seq, in which each molecule is tagged with a barcode before PCR, so all sequencing end results could be traced back to each molecule by the barcodes. This may provide a more accurate estimation of the numbers of original MtDNA with or without the deletion.

https://www.takarabio.com/products/next-generation-sequencing/dna-seq/molecular-tagged-library-prep-for-illumina

[Assa Yeroslaviz]

thanks for the explanation, but this was not my question. I am not interested in the biology behind it. I would like to know if, when using the tool delly for quantifying breakpoints, the problematic of having the same molecules multiple times is accounted for.

Can delly quantify the number of copies, or just output how many breakpoints exit in the data set?

thanks

[Vitis]

I'm a bit confused. Usually variant callers like Delly would give a "depth" parameter for the variants. Isn't that what you're looking for? Of course, "depth" is not number of copies or number of molecules, they're just related. You need other approaches to track down the number of molecules.