Next generation sequencing (NGS) is a commonly used technique in genomics research projects. There is an increasing need for all stages of sample manipulation for NGS to be automated, from sample plating through to library preparation and final pooling before sequencers are loaded. Although many of these steps can now be automated, the size selection step presents more of a challenge. Many NGS applications require tight distribution of fragments within a specific range. Double size selection using Beckman Coulter’s SPRIselect® beads can achieve very tight fragment size distributions and is fully automatable in a 96-well format.
Here, the automation of size selection using these beads on the Biomek® FX Liquid Handler (BFXP) is described. The BFXP has a hybrid configuration and is equipped with a multi-channel 96 pipetting head and Span-8 Pod with 1000μl syringes. The Span 8 probes transfer SPRIselect beads, ethanol and elution buffer and the multichannel pipetting head removes supernatant and transfers the final material eluted. Where libraries of multiple size ranges are required, users can apply multiple reagent:sample ratios to select a different size range for each well of a 96-well plate. The beads selectively bind fragments according to these ratios and adjusting the ratios enables fragments outside of the desired size range to be efficiently removed. The flexible SPRIselect kit workflow can be easily adjusted to remove small fragments, large fragments or both. The method’s user interface is easy to use and provides the operator with control over selection type, sample input volume and binding and elution parameters.
Biomek® FXP Laboratory Automation Workstation
This automated size selection method generates highly reproducible results and after sequencing on a HiSeq instrument, high quality data can be obtained. Appropriate size selection enables more efficient sequencing yields to be obtained because smaller and larger fragments do not contribute equally to the clustering or emulsion PCR step. Genome assemblies are also more accurate as a large fragment range can result in incorrect alignment/assembly if the paired read interval is not well defined.
The main advantages of the automated SPRIselect method over electrophoresis-based approaches are time and cost savings. When using the SPRIselect method on a single BFXP, it takes around two hours to perform size selection on 96 libraries. This compares with around ten hours when four SAGE Pippin instruments are used. Furthermore, the cost of consumables is around 5 to 7 times lower using the Biomek SPRIselect method.
To find out more about this size selection automation solution click here.
About Beckman Coulter
Beckman Coulter develops, manufactures and markets products that simplify, automate and innovate complex biomedical tests. More than a quarter of a million Beckman Coulter instruments operate in laboratories around the world, supplying critical information for improving patient health and reducing the cost of care.
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