Thursday, 10 July 2014

Agilent’s Clinical Meeting, Haloplex and SureSelect

Agilent’s Clinical Meeting, Haloplex and SureSelect

I recently attended the Agilent Clinical Meeting in London which gave some very informative presentations on the extent to which Next Generation Sequencing is aiding diagnosis of disease and screening in the clinic. Clinical genetics labs need to be able to provide diagnostic tests which have a very rapid turnaround time that are also cost effective.

Many diagnostic tests are currently based on sequencing a specific gene and using Sanger sequencing. However, many people talked about how they are developing panels for targeted sequencing along with studying the exonic regions by exome sequencing.  Despite the advances of NGS in the clinic, it was clear that whole genome sequencing is where we want to be heading, to get a complete picture. Unfortunately right now, it is not affordable enough.

After attending this conference it was interesting to see how other labs are using Agilent’s Enrichment and panel solutions so thought I would summarise the technologies here.

Haloplex Target Enrichment

What is Haloplex?
HaloPlex is a Target Enrichment System which can be used for the analysis of genomic regions of interest and is aimed for studying a large number of samples.

How does it work?
1.The workflow appears quite simple, starting with DNA fragmentation using restriction enzymes. 

2.Probes which are designed to both ends of a DNA fragment are hybridised to form circular DNA molecules.

3.There is a clean-up step using magnetic streptavidin beads which captures only those fragments containing the biotinylated Haloplex probes. The circular molecules are then closed by ligation.

4.Finally, PCR is used to amplify the targeted fragments ready for sequencing.

What can I enrich for?
SureDesign software can be used to design these custom panels for specific genes or for thousands of exons of interest.

Several clinical labs described how Haloplex technology is enabling them to design diagnostic tests based on screening for specific disease causative genes. Its popularity seemed to be down to its ability to permit a fast turnaround time due to the reduced amount of sample preparation required.

SureSelect Target Enrichment

What is Sureselect?
Agilent’s SureSelect technology enables you to look at the whole exome or at a targeted panel.  It has become a very useful tool in focusing on familial disease loci and for validation of whole genome sequencing. 

How Does it work?
The SureSelect workflow involves a shearing step of gDNA followed by library preparation incorporating adaptors required for sequencing and indexes for multiplexing. Regions of interest are selected for by a 24hour hybridisation step with biotinylated RNA library baits followed by a cleanup step using magnetic streptavidin beads. The baits can be custom designed using Agilent’s SureDesign software. PCR is then used to amplify these regions which are then ready for sequencing.

Exomes in the Genomics Core

Here in the Genomics core, we are currently using Illumina’s Nextera Rapid Exome kit for Exome sequencing and Fluidigm Access Arrays for generating libraries for targeted sequencing.

Agilent have recently released a new SureSelect kit, SureSelectQXT which combines a transposase-based library prep, followed by target enrichment. We have just received one of these kits and will soon be testing this in the lab.


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