Exome Sequencing vs Target Region Sequencing

[Marco0208]

Hi guys

What is the difference between Exome sequencing & Target region sequencing ?

I know roughly exome sequencing only sequences exons and Target region sequencing sequences specific regions/ genes.

But what confuses me is the methods and procedures.
Both Agilent Sure-Select kits and NimbleGen Kits are involved in both sequencing methods ..... and are they the same workflow ?

Cheers

[frostzwerg]

Hi Marco,

In principle yes, exome sequencing and target region sequencing are the same, using the same workflow!

In more detail, exome enrichment is one part of target region enrichment (if you define your target region as the exome). If you define your target region as say 100 genes of interest, then you have to use some modified bait sequences to enrich the targets you want to sequence.

[Marco0208]

Hi

Thanks for the reply.

Strange because my colleague told me the methods for both sequencings are different !!! Anyway, i know that at least Exome is for Exon sequencing and Target Region sequencing is for any genes.

One of reasons why i though both methods are the same is because of the capture platform .....

For Exome Sequencing, it saids Agilent SureSelect Human ALL & NimbleGen SeqCap EZ Exome

For Target Region Sequencing, it saids Main Capture arrays/kits OR personalized capture kits from Agilent SureSelect and NimbleGen Kits

Are the methods = same???

But i was asked to present on both topics !!! I am getting more confused because i always thought they were the same apart from the targeted genome !!!

PLEASE HELP !!!!

[TonyBrooks]

Exome sequencing IS targetted region sequencing. The targetted region is the exome (exons). Baits are designed against those regions to pull down library fragments that come from those regions of the genome. At the moment, due to enrichment size (tens of Mb) this is really the only way to enrich for the exome.
Targetted region sequencing can be done in the same way, using the same protocol, but by requesting other genomic regions (any thing above a few kb). These regions can be a sub-set of the exome (you may not want to sequence every gene) or perhaps you want more intronic regions or UTRs from certain genes that aren't on the exome panel of choice. There are large economies of scale so unless you plan on running hundreds of custom regions it's sometimes cheaper to go for an off the shelf exome.
The sequencing methods of both will be the same (although obviously, if you're sequencing smaller regions, you don't need as many reads). In fact, for most applications you rarely need to alter how you sequence, just how much.

However, there are other methods for targetted sequencing (really only suitable for smaller regions of interest) such as amplicon sequencing. Examples of these are Illumina's TruSeq Custom Amplicon, Agilent's Haloplex, Raindance, Fluidigm and AmpliSeq from Life.
Amplicon sequencing can't enrich for regions as large as an exome (at this moment in time).

[buckybadger]

The most basic differences between the Agilent SureSelect and NimbleGen Kits are that the Agilent kits use biotinylated RNA oligonucleotide probes with 65 deg C hybridization temperature, while the NimbleGen Kits use biotinylated DNA oligonucleotide probes with 47 deg C hybridization temperature. There will also be differences in the buffers they use. Another, often under-appreciated, difference between the two products is the bioinformatics expertise and algorithms behind the probe selection process. Both can use Illumina compatible sequencing libraries as input.

Here are some relevant links that were recently published:

http://www.ncbi.nlm.nih.gov/pubmed/23814499

http://www.ncbi.nlm.nih.gov/pubmed/23547016

http://www.ncbi.nlm.nih.gov/pubmed/21955854

http://www.ncbi.nlm.nih.gov/pubmed/21947028

Cheers,

--BB