panel resource for Whole Exome Sequencing data

[ahwanpandey]

Hello,

I was hoping to get some help regarding a panel resource for my WES data.

Assay = Whole Exome
Sequencer = NextSeq 2000
KIT = SureSelect XT HS Clinical Research Exome V4 (S34226467)
Cancer type = HGSOC

Number of samples

• 5 Fresh Frozen (FF)
• 5 FFPE
• 4 Germline

I understand that I should only use tumor samples for the panel creation and also do it separately for FF and FFPE. Which means that I onyl have 5 samples for this purpose.

I don't think these are good enough numbers to create a robust panel resource. Do you have a resource available that is compatible with my data that you could share, at least for the FF samples?

Any advice would be very helpful!

Thanks,
Ahwan

[p-priestley]

5 samples is insufficient and risky. Even 14 samples is not great.

With such a small data set, if you absolutely want to goa ahed, I would suggest to definitely use all 14 samples for the panel creation and tolerate the differernces between fresh and FFPE. I absolutely don't think this will be 'robust' for copy number but you may get some workable results

We don;t have experience with that specific exome kit sorry.

[ahwanpandey]

@p-priestley , thanks for the quick response! When you say copy number won't be robust, so would small variant calling be at least more usable? I totally understand that in any case it would be risky.

If I were to try to find public datasets to boost the numbers, would the Sequencer also have to be the same or is it just the kit that needs to be the same? I am assuming both?

[p-priestley]

Small variants should be fine.

If you have a very hybrid data set it may make the copy number normalisation worse, so I would be cautious there also