Questions about whole-exome sequencing on NextSeq 500

[newtoseq]

Hi everyone,

My lab is looking into performing whole-exome sequencing on a small sample of human subjects on the NextSeq 500. I am responsible for researching the budget involved in such an endeavor and, as a newbie to this subject, would like to seek your advice on the number/type of sample prep/reagent kits to achieve our sequencing goals.

We would like to whole-exome sequence 4-8 (depending on total costs) human subjects at >100x coverage, pair-ended read using the Nextera Rapid Capture Exome Kit and, ideally, the High Output 300 cycle NextSeq Kit.

So, if we use 1 Nextera Rapid Capture Exome Kit (8rxn x 6plex), which according to documentation at 6plex can sequence 6 exome samples using NextSeq 500 High-Output kit, and 1 NextSeq Kit, High Output (300 cycle), can I whole-exome sequence up to 6 unique human subjects at >100x coverage with pair-ended read?

edit: As a follow up question, I'm assuming that 1 Nextera Rapid Capture Exome Kit (8rxn x 6plex) can support sequencing of up to 48 exome samples, by the 8 reaction x 6 plex criteria? I apologize for my ignorance, thank you very much for your help.

Thank you for your help.

[Brian Bushnell]

Are you locked in to the NextSeq platform, or do you have the possibility of using something else?

[newtoseq]

Are you locked in to the NextSeq platform, or do you have the possibility of using something else?

Hi Brian, at this point, we are currently only looking at using the NextSeq 500. Thank you.

[Brian Bushnell]

I encourage you to look at this thread.

But that aside... I can't help you with the economics. In fact, I think human resequencing is one area where NextSeq might possibly be useful, though it highly depends on the price. Unless NextSeq is vastly cheaper than HiSeq per bp, it's a bad idea, since the error rate is currently so high. Particularly for exome capture, where the coverage is even more highly variable than usual for Illumina, forcing you to call variants at very low coverage.