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Target-enrichment strategies for next-generation sequencing produce different results, according to researchers from the University of Miami (UM) Miller School of Medicine and Life Technologies. The results could help researchers choose a capture method that best suits their experiment.
“We see what’s performing best in our hands and talk to our colleagues elsewhere to find out what’s performing best in the current generation,” said study author Dale Hedges, an assistant professor at UM. “We try not to get locked into one particular platform. It is a field that is rapidly changing.”
Agilent’s SureSelect, which uses streptavidin-coated magnetic beads to capture hybridized genes with biotinylated RNA substrates, had the highest on-target enrichment efficiency and the highest Pearson correlations in depth coverage across six sequencing samples. Nimblegen, which uses a microchip to capture hybridized genes, performed similarly at read depths at 20x and below.
Although having lower on-target efficiency overall, RainDance and Nimblegen SeqCap had a tighter distribution of coverage about the mean than Agilent’s SureSelect. Furthermore, the Raindance strategy was considered the most flexibility in terms of where the primer can be placed in the target sequence, allowing the capture of repeated regions that are not unique in the genome.
But these performances may change in the future as new options and improvements to existing techniques continue to be released.
The paper, “Comparison of three targeted enrichment strategies on the SOLiD sequencing platform,” was published 29 April 2011 in PLoS ONE.
