Illumina Rapid capture vs. Agilent SureSelect Exon

[JER]

I am currently using Illumina's Nextera Rapid capture Enrichment kit for WES Library prep but am about to start a new project and was wondering whether it is worth switching to one of Agilent's SureSelect Exon Kits?

I've read up on this and it seems a lot of people use Agilent over Illumina, this is probably due to slightly better coverage etc but the Illumina requires less gDNA and is generally cheaper per sample. Does anyone have any recommendations either way?

Also, are the Agilent kits any good for DNA from FFPE samples?

Thanks

(P.S. there is a pdf attached of a paper comparing Agilent SureSelect, Illumina Nextera, Illumina TruSeq and NimbleGen Kits)

[idedios]

I've worked with both Agilent's SureSelect QXT workflow as well as Illumina's Nextera Rapid Capture and I found Agilent's to be quicker and easier to set up. The data was also very clean and it only required one hybridization step as opposed to Illumina's two.
Another nice thing with Agilent's kit is that you can run small batches of samples without wasting extra reagents whereas Illumina's kit forces you to run in batches of 12 or else you waste oligos and capture reagents.
The panels I ran were both custom designed (same design for both). Neither company officially support FFPE however it still worked out rather well for me as I ran FFPE exclusively with these kits.
One odd thing to note is Agilent's kit has a weird problem with the 2nd PCR before sequencing where if you run too many PCR cycles, the sequencing will fail completely (no signal from the cameras). In my case I ran 14 cycles instead of the recommended 12 for my library size since there was confusion about how many cycles to run for a given library size.
So in conclusion you should use Agilent if you want to work in batches smaller than 12 samples per run.

[Pistachio]

Thank you very much. You are so helpful.. ~

[ymc]

Thanks for idedios's input. No wonder SureSelect is dominating this market.

Do you guys know whether there are official hg38 bed files for SureSelect exome kits? I went to the eArray site but I could find only hg19 bed files. Are hg38 files also there? Anyone knows?

[anujgupta]

QXT with FFPE

I've worked with both Agilent's SureSelect QXT workflow as well as Illumina's Nextera Rapid Capture and I found Agilent's to be quicker and easier to set up. The data was also very clean and it only required one hybridization step as opposed to Illumina's two.
Another nice thing with Agilent's kit is that you can run small batches of samples without wasting extra reagents whereas Illumina's kit forces you to run in batches of 12 or else you waste oligos and capture reagents.
The panels I ran were both custom designed (same design for both). Neither company officially support FFPE however it still worked out rather well for me as I ran FFPE exclusively with these kits.
One odd thing to note is Agilent's kit has a weird problem with the 2nd PCR before sequencing where if you run too many PCR cycles, the sequencing will fail completely (no signal from the cameras). In my case I ran 14 cycles instead of the recommended 12 for my library size since there was confusion about how many cycles to run for a given library size.
So in conclusion you should use Agilent if you want to work in batches smaller than 12 samples per run.

can you share your experimental experiences with QXT for FFPE? Did you modified anything? pls share it to [email protected]