How to go fishing in the deep end of the gene pool

AN APPLICATION note now available from Oxford Gene Technology provides scientists with valuable guidance on the use of targeted probes to improve data quality in next-generation sequencing.

The note, titled Fishing for variants in the deep end of the gene pool, discusses the design of customised probes (so-called ‘bait probes’) to reduce off-target noise and optimise the detection of variants.

This approach of custom bait design can target specific regions of the genome for variant detection, rather than investigating the whole genome or exome, and improve call accuracy by substantially increasing the depth of coverage.

High-throughput processing of samples is enabled, reducing costs significantly, and data processing is streamlined because large tranches of irrelevant sequencing data are simply not generated.

A further advantage, says OGT, is that well-designed probes can be used to investigate GC-rich areas of the genome, ensuring studies are not biased towards low-GC regions.

There remains a place for whole exome sequencing, in areas such as the analysis of Mendelian disorders and GWAS studies, but custom designs offer significant advantages where the biological question is more focused.

However, the company points out, custom bait design is not a trivial task, and poorly designed probes can produce unusable results. The company recommends its Genefficiency targeted sequencing services to create custom bait, which it says will ensure accurate, unbiased results with true biological insight.

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