Whole genome sequencing or whole exome sequencing- which is better and why?

Question

[Sujata]

if genomic DNA is extracted from tissues, and the goal is to find variants such as SNP, indels, CNVs-which is the preferred method- whole exome sequencing or whole genome sequencing and why?

Under what cases can we use RNA sequencing to find variants?

[lakhujanivijay]

Consider reading this link . And this is not a forum rather a question.

[Sujata]

Right I will post it in questions section. Thank you for the link

Answer 1

[WouterDeCoster]

if genomic DNA is extracted from tissues, and the goal is to find variants such as SNP, indels, CNVs-which is the preferred method- whole exome sequencing or whole genome sequencing and why?

SNPs and short indels can be called both using WES and WGS. However, you can only call variants if they're sequenced, which with WES is limited to the exome, obviously. If you are interested in non-coding variants you need WGS. CNVs and other SVs are hard with short-read WGS and nearly impossible with WES.

But of course there is also a difference in price, so your budget will play a role as well.

Under what cases can we use RNA sequencing to find variants?

You should never design an RNA-seq experiment with the aim to find variants. However, if RNA-seq is what you have you can look at variants, but take into account that it's far from optimal and won't give you the best results.

[ATpoint]

Adding on this, you should (and probably must) also choose between short and long read sequencing. As WouterDeCoster says some structural variants will be difficult or impossible to find with short reads whereas SNPs are the realm of short reads.

[German.M.Demidov]

I'd add - if the goal is the detection of something small (such as tumor sub-clonal SNVs) - ultra-deep WES/Targeted Panel Sequencing of important genes are way better than WGS.

[WouterDeCoster]

You are confused. You claim WES/panel is better than WGS here, while the difference is just the sequencing depth. If you do ultra-deep WGS you would find the same (and much more!). It's not a matter of technology, but of depth.

[German.M.Demidov]

ah, yes, from this point of view - sure. however honestly I'd strongly prefer to work with 10.000x panel-based liquid biopsy rather than 10.000x WGS - I honestly don't know how will I operate with the file of such size just to extract 100 important positions.

[WouterDeCoster]

Oh yes, if you already know what you are looking for then a targeted panel is fine.

[Sujata]

Where does Targeted Panel sequencing come in terms of library preparation in sequencing and which sequencing platform would be ideal for finding mutations in cancer?

[German.M.Demidov]

As discussed above, there is no single answer =( It can be 1) finding structural variants in cancer - and TPS sucks here, 2) finding SNVs and CNVs - then clinics usually use custom panels of 100-800 cancer driver/supressor genes, 3) tracking of potential relapse using ultra-deep liquid biopsy - the panel is constructed for each patient separately (well TPS of the same panel may be used - but it is difficult to achieve 100.000x there) - and so on...

[WouterDeCoster]

Where does Targeted Panel sequencing come in terms of library preparation in sequencing

What does that question mean?

[ATpoint]

I strongly recommend that Sujata spends time on the basics of sequencing platforms and applications before making any business decisions on what kit/platform/strategy to use for the project.

[Sujata]

I am starting from basics and that is why my questions may not make sense. I am trying to understand how different technologies work and questions like... (i) How does TPS work? How is it different? coverage versus depth?

[Sujata]

How is library preparation done for TPS? how do TPS works? Please provide animation or article.

[German.M.Demidov]

https://youtu.be/zuWmekivQ4c