About Whole Exome Sequencing analysis

Question

[kwanghoon]

Hi,

I'm trying to analyze Whole Exome Sequencing data between two groups.

I come here to get some advise about analysis.

Using variant call data, I did some filtering. So I got filtered variants list.

I draw an oncoplot using pathogenic & likely pathogenic variants, did some mutational signature analysis, CNV analysis and some statistical analysis.

I have many "Uncertain Significance(VUS)" variants, so I want to do some statistical analysis.

I made a graph that has variant counts of genes like below.

What kind of statistical analysis to this data??

Thank you.

[LauferVA]

What kind of statistical analysis to this data??

Do not proceed like this. Instead, you need to determine what the goal of your analysis is. Then, you choose the best powered statistical test for that question.

[kwanghoon]

Thank you for reply.

I have two group A and B.

I want to know what kind of genes are significantly different between groups.

I'm very new at these analysis.. I don't know what I have to do...

[Ram]

Do not delete posts that have received feedback.

[kanika.151]

Hi,

How do you know they are 'VUS' variants? They were classified as 'VUS' by using a tool or by a person using any guidelines such as 'ACMG'?

Also, it is normal to have many 'VUS' variants. I would further classify these 'VUS' variants into 'weak VUS' and 'strong VUS' candidate variants.

[LauferVA]

Please read the following organizations' statements on VUS for an introduction.

ClinGen ACMG and AMP ExAC ClinVar

for a brief introduction to this field. There is substantial clinical, research, and for-profit interest in how variants are classified. I think reflecting on why that could be true, then investigating if you were right, could be instructive.