Chromosomal translocation, which NGS method appropriate

[deepbiomed]

Hi,
if one only had DNA available, how confident would we be in being able to call a translocation using either WGS (low coverage) or WES?

[r.rosati]

My two cents ... "It depends".
If it's an unbalanced translocation, in a condition where this is the sole genomic imbalance, then your best bet would actually not be NGS but microarray CGH, which will identify the copy number alteration leading you to a plausible breakpoint for the translocation. WGS and WES might give you an idea too, but not with the same detail.
If it's a balanced translocation, and in WES you're working with a hybridization capture technology for library preparation, then you might see it if the breakpoint is within or very proximal to an exon (and it doesn't interfere with the probe). You will lose it if it's in an intron and far from the flanking exons.
Balanced and you're doing WES using amplicon-based library prep(e.g. Ampliseq) - you would need the breakpoint to be, again, within or extremely close to an exon, and you must be lucky enough that the primers that would amplify it are in the same pool.
Balanced and you're doing WGS - you have the chance of picking the breakpoint within an intron, if it's not buried inside a repetitive element, but low coverage might hamper the call. You might have some more chances if you know what you're looking for, hence not relying solely on algorithms. Mate pair reads might help you.

EDIT: I'm re-reading it and I read like a fortune cookie. This is actually quite appropriate.

[pmiguel]

My two cents ... "It depends".
[...]
Balanced and you're doing WGS - you have the chance of picking the breakpoint within an intron, if it's not buried inside a repetitive element, but low coverage might hamper the call. You might have some more chances if you know what you're looking for, hence not relying solely on algorithms. Mate pair reads might help you.

EDIT: I'm re-reading it and I read like a fortune cookie. This is actually quite appropriate.

Would your answer change if the WGS coverage was 30X, instead of "low"?

--
Phillip

[luc]

Not cheap, but a 10X Chromium Genome library prep and sequencing would be great option for a balanced translocation. It requires 30x coverage though.

[r.rosati]

Would your answer change if the WGS coverage was 30X, instead of "low"?

--
Phillip

In my humble opinion I would think that this would improve dramatically the chance to find the translocation algorithmically (as opposed as curating the data manually). Still, if the breakpoint is within a repetitive element that's been rearranged with a homologous sequence, the effort could still be in vain in my opinion.