With Xdrop™ in your lab, your target enrichment becomes as easy to set up as a standard PCR analysis.
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Coverage graph obtained when sequencing Xdrop™ enriched samples on Oxford Nanopore MinION.
Left: region spanning 10 kb around the Target ID (amplicon designed for detection) Right: region spanning 100 kb around the Target ID. This specific experiment was designed to enrich for a portion of the human gene BRCA2.
Even though long-range PCR is widely used, this method can be challenging especially when trying to uncover large regions (tens of kilobases). To fully unravel sequence information of large regions, multiple long-range PCR primer sets are needed, and each primer set needs to be independently optimized.
This process can both be laborious, time-consuming and difficult for large genomic regions, especially those which contain difficult-to-PCR regions.
Failures and long-range PCR primer re-designs make the process time consuming and the process requires extensive hands-on time. Furthermore, PCR product - and sample management are challenging, as well as repeated PCR product quantifications, normalizations, pooling and library preparation. Also, long-range PCR requires full sequence knowledge of the targeted region.
Other technologies for target enrichment are for example custom DNA or RNA probe based bait enrichment or PCR based library preparations.
These methods can however be difficult to apply to certain genomic regions, synthesis of baits or primer pools often cause long delivery times, are generally expensive, and have minimum sample number restrictions which may not fit with the project size. They also demand full sequence knowledge of the targeted region.
Xdrop™ DNA amplification is PCR-free which reduces bias and errors typically found in PCR-based methods.
Only limited sequence information is needed for each region making Xdrop™ a perfect choice for de-novo gene region sequencing based on transcriptome data or target organisms where genome information is limited (e.g. plants).
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