Version history and design files for exome kits from Agilent, Roche(Nimblegen), and Illumina

Question

[predeus]

Hello all,

I am working on comparison of exome kits and came to understand that it can be quite hard to understand what's offered in the market and what are their relative advantages. So I made this topic dedicated to collecting of information about exome kits from the three major providers: Agilent, Roche (formerly Nimblegen), and Illumina. Only whole exome kits and slightly extended versions of them are considered. I would also like to make a collection of all available design files, and would ask you to share some of the rarer design files if you have them. I'll make them publicly available once I have the collection checked and properly annotated.

I would also only consider only hybridization-based methods and not the amplicon-based ones (HaloPlex, AmpliSeq).

It's often confusing to figure out the version history and correct type of the product, so please correct me if you think I'm wrong with the description or version of the kit. I also still have some questions that are not clear to me - please see below in bold.

1. Agilent. Currently Agilent is by far most poplar provider of exome and offers the broadest selection of exome kits. More than 70% of the ExAC exomes are done using Agilent kits.

As it was mentioned on biostars before, you can get access to the design files for Agilent by registering at EArray and then navigating to SureSelect DNA - Agilent Catalog:

Below is a screenshot of what's available:

The framed names are variants of WES - with or without extra regions.

What's interesting is the concept of "Clinical exome" - this is just a regular whole exome, but with (supposedly) better coverage of clinically relevant genes.

What's missing is design files for versions 1-3. If anybody knows where to get them, please let me know.

I also am not certain what version of Agilent became "Agilent Human AllExon 50M", instead of the older 38M version. Several exome comparison papers mention Agilent 50M. I think the first "Agilent 50M" kit was version 3.0; please let me know if you have more information.

2. Roche/Nimblegen. Roche currently is offering three WES solutions:

SeqCap EZ Exome Kit v3.0

SeqCap EZ MedExome

SeqCap EZ MedExome with extended mitochondrial design

The difference here, again, is that MedExome is supposed to have better coverage of clinically relevant genes.

What is confusing is that MedExome and MedExome+mito all point to the same design archive as SeqCap EZ Exome Kit v3.0.

If anybody knows where could one get design files for versions 1 and 2, as well as proper MedExome design files, please let me know.

3. Illumina. Illumina is offering four major WES solutions:

Nextera Rapid Capture Exome

Nextera Rapid Capture Expanded Exome

TruSeq Exome

TruSeq Rapid Exome

Unfortunately, their design does not have explicit versions attached to them, but in file names one can tell that the current version of the regular exome is 1.2. Expanded 62M exome has extra UTR coverage, similar to ones from Agilent and Roche. Other three apparently share the same 45M design. What is interesting is that original Illumina design had a lot of UTRs included, which is reflected in some of the earlier exome platform comparison papers

.If anybody can share some knowledge about Illumina versions, as well as earlier Illumina design files, I would be grateful.

Thank you for any input. All discussions are welcome.

[jon.klonowski]

Hi, How can I access these file at this point? the links are taking me to a long in page where I need a validation key (?) I am looking for interval files/exome build for SeqCap EZ MedExome

[jon.klonowski]

https://sequencing.roche.com/en/support-resources/discontinued-products/seqcap-ez-medexomekit.html

under "Design Files"

[GenoMax]

Are you sure? I click on file links and was asked to save the file for both links. I am not logged in to Roche site.

Answer 1

[tjduncan]

Hi,

This is a great list of exome capture providers to use as future reference. I included a bit of info on two additional exome capture providers in the message below.

One of the biggest "up and coming" exome capture providers is IDT. Many users are very familiar with them for their other oligo work and I hear that they have a very good exome product.

xGen® Exome Research Panel v1.0

The Exome Research Panel spans a 39 Mb target region (19,396 genes) of the human genome and covers 51 Mb of end-to-end tiled space. All probes in the panel are manufactured using GMP standards. Mass spectrometry and OD measurements are taken for each probe to ensure appropriate representation of the correctly manufactured probes in the pool.

Also about a week or so ago I saw that Twist Biosciences has launched an exome kit:

Human Core Exome Enrichment System

I am not sure how their enrichment functions (what is special about it) and I have not heard of anyone who has used it.

[predeus]

Thank you, this is useful. The field is changing so rapidly. It's good to keep track of what's going on.