Adaptive Sampling and digital panels

For targeted sequencing with digital panels, powered by Adaptive Sampling, we recommend the PromethION devices as they provide the necessary compute for efficient on-sequencer enrichment.

The PromethION 2 Integrated enables sequencing on two independent flow cells, providing streamlined, affordable sequencing for every lab. For higher-throughput requirements, the PromethION 24 offers sequencing on up to 24 independent flow cells, supporting the analysis of thousands of samples per year.

Ready-to-use research-use-only digital panels can be modified in minutes with our online Digital Panel Designer (coming soon). Simply select the digital panel you want to modify and customise your targets by either adding or removing any genes or regions of interest. The designer will then generate the files needed for a successful Adaptive Sampling run. Find out more.

Our sequencing software MinKNOW performs real-time data acquisition and basecalling during sequencing, including methylation detection. After sequencing, your data can be analysed using our EPI2ME workflows or via instructions in our somatic analysis bioinformatics guide, depending on your application. View our getting started guide for more information.

Adaptive Sampling doesn’t require upfront design or purchase of amplicon primers or hybrid-capture probes for target enrichment, removing the need for multi-day wet-lab enrichment and optimisation workflows. Instead, a digital panel (BED file) defining the regions for enrichment is uploaded to MinKNOW, the sequencing software, for streamlined on-device target enrichment.

During sequencing, the start of each DNA molecule is analysed in real time against the regions defined in the digital panel. Molecules matching a target continue to be sequenced, while non-target molecules are rejected so another molecule can enter the nanopore. This increases coverage across regions of interest, while the initial sequence generated from rejected molecules provides low-pass whole-genome data that can support analysis of copy number changes, large chromosomal abnormalities, and global methylation patterns.

Because PCR is not required during library preparation, native DNA is sequenced directly, retaining methylation information. Long nanopore reads (approximately 6–10 kb using the recommended Adaptive Sampling protocol) can support the characterisation of repeat expansions, structural variants, fusions, and other complex genomic regions.

Read more about how Adaptive Sampling works.

Adaptive Sampling can target anything from individual genes to large genomic regions or whole chromosomes. For optimal enrichment, we recommend targeting between 0.1–5% of your reference genome. View our Adaptive Sampling technical guide for more information.

Yes. Adaptive Sampling sequences native DNA without requiring PCR-based target enrichment, preserving DNA methylation information for analysis alongside the underlying sequence. This allows you to investigate methylation together with targeted and low-pass whole-genome data, providing a comprehensive multiomic view from a single sequencing run.

Find out more about our gold-standard methylation detection.

Yes. Barcoded samples can be pooled and sequenced together using Adaptive Sampling, allowing multiple samples to be analysed on the same flow cell. The number of samples you can multiplex will depend on the sequencing output and coverage required for your application.