Question: Can I use custom targeted assays with Genome libraries?
Answer: Yes. It is possible to use a custom bait set with our Exome protocol. For Exome applications, a Demonstrated Protocol using the Agilent SureSelectXT Human All Exon V6 Reagent Kit with our 10x Genome workflow can be found here: https://support.10xgenomics.com/genome-exome/index/doc/demonstrated-protocol-chromium-exome-demonstrated-protocol-v2-chemistry
This protocol can be modified to accommodate other bait sets by substituting the Agilent probes and capture protocol for the desired bait set. In general, the bait set manufacturer's instructions can be followed for capture, although we recommend using the maximum input allowed by the capture protocol to maximize recovery. Once the capture has been performed, the Post Capture Amplification Kit can be used to amplify the library for sequencing.
We have guidance for using custom baits here: https://support.10xgenomics.com/genome-exome/index/doc/technical-note-target-enrichment-using-custom-baits-with-the-chromium-genome-reagent-kit
The sequencing depth should be adjusted based on panel size. We recommend sequencing to 60x effective coverage, which is dependent on the panel size and the on target rate for the panel.
Products: Genome, Exome