Improving NGS Accessibility
Blog Dec 01, 2014
Integrated DNA Technologies (IDT) recently introduced xGen® Predesigned Gene Capture Pools and Plates, enabling researchers to create target capture panels in-house.
To learn about the benefits of customization, and how the Gene Capture Pools and Plates can help make sequencing more affordable, we spoke to Rami Zahr, PhD, NGS Product Manager at IDT.
AM: IDT recently introduced xGen® Predesigned Gene Capture Pools and Plates. Can you tell us a little about these?
RZ: It’s a fascinating time for next generation sequencing, with new tools making this technology increasingly accessible for smaller labs. In line with this shift, we’ve focused on providing researchers with access to affordable target capture for NGS experiments, through our xGen® Lockdown® Probes, and now, xGen® Predesigned Gene Capture Pools and Plates.
xGen Lockdown Probes are individually synthesized, 5’ biotin modified DNA oligonucleotide probes (60–120 nt), designed to target the researcher’s requested genomic regions. We use these probes to create our xGen Predesigned Gene Capture Pools, where each probe pool targets the coding region of a single human gene. xGen Predesigned Gene Capture Pools are available for every human gene. What is more, we can supply these gene probe pools in separate plate wells. Thus, researchers can customize their target capture experiment to their specific sets of gene targets.
AM: What are some of the benefits of customization?
RZ: Being able to pick and choose the most interesting sections of the genome saves time and resources compared to whole genome sequencing. Regions of interest vary incredibly between different investigations, and will even change as a study evolves. Frequently, groups within a single laboratory study related biological pathways or diseases, where the genomic regions they need to target have both overlapping and unique targets.
Until now, researchers have been limited to two main options: affordable but inflexible off-the-shelf panels, or expensive custom probe pools. Off-the-shelf panels may include unneeded probes, requiring the researcher to waste resources on sequencing on regions that are not of interest to them. Additionally, these commercial panels may be missing probes to key targets, requiring the purchase of additional probes.
Purchasing custom probe pools to a specific set of targets also has drawbacks: extended time for synthesis and delivery of the probe pools, costly price, and once received, time and labor intensive protocol optimization.
xGen Predesigned Gene Capture Pools and Plates introduce a new level of flexibility. These stocked pools are ideal for creating customized target capture panels for 10 or more genes, or for providing probes to augment target breadth and enhance performance of existing panels; for example, by increasing depth and uniformity of coverage. Because they have already been designed and synthesized, they can be obtained quickly.
AM: What are some of the advantages the Gene Capture Pools and Plates offer over existing products?
RZ: Laboratories can obtain a plate of individual gene probe pools and create their own target capture panels, with one group using one subset of probes, and another group using an overlapping but different set. As their studies continue, the scientists can create new panels, adding or removing probes for particular targets as these targets are deemed relevant or not.
We also offer the xGen Predesigned Gene Capture Pools and Plates in two different reaction sizes, 16 reactions and 96 reactions, so that researchers can match them to their study size. Researchers typically optimize their data in the initial experiments and, often, do not require the amounts of probe provided in off-the-shelf panels. By having reaction size options, researchers can purchase just the amount of probe they need—mitigating expensive waste.
AM: IDT aims to make sequencing more affordable and practical for a wider range of applications. How do the Gene Capture Pools and Plates help achieve this?
RZ: Every researcher has different needs, yet for specialized studies, customized panels were previously the only option. As we mentioned, these have always been expensive, limiting their application to the largest, well-funded labs. xGen Gene Capture Pools and Plates let researchers and core labs generate relevant, custom gene panels in-house, and in appropriate reaction sizes. With this product, IDT has reduced the cost of custom panels dramatically, making NGS much more accessible to the entire scientific community.
For more information please visit www.idtdna.com.
Rami Zahr was speaking to Anna-Marie MacDonald, Editor for Technology Networks.