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Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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Fine-tuning the Size and Minimizing the Noise of Solid-state Nanopores

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Enhancing nanopore adaptive sampling for PromethION using readfish at scale.

Rory Munro¹, Alexander Payne¹, Nadine Holmes²

¹School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom.

Genome Research

|January 30, 2025

Summary

This summary is machine-generated.

Oxford Nanopore Technologies adaptive sampling, a DNA selection tool, has been enhanced in readfish for the PromethION sequencer. This enables efficient genome analysis, including copy number and structural variations, on a large scale.

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Sequencing of mRNA from Whole Blood using Nanopore Sequencing

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Published on: June 3, 2019

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Oxford Nanopore Technologies (ONT) sequencers offer adaptive sampling for targeted DNA molecule selection.
The readfish tool previously supported adaptive sampling on smaller-scale ONT sequencers.
Industrial-scale sequencing requires robust and efficient targeted enrichment methods.

Purpose of the Study:

To enhance the readfish tool for full functionality on the industrial-scale PromethION sequencer.
To enable both standard and barcode-aware adaptive sampling on the PromethION.
To demonstrate the utility of enhanced readfish for large-scale human genome analysis.

Main Methods:

Implementation of readfish features for PromethION compatibility.
Utilizing standard and barcode-aware adaptive sampling strategies.
Performing coverage enrichment and analysis of multiple human genomes for structural variations.

Main Results:

Readfish now fully supports adaptive sampling on the PromethION platform.
Demonstrated effective coverage enrichment for targeted genomic regions.
Successfully assessed copy number and structural variations across multiple human genomes on a single PromethION flow cell.

Conclusions:

Enhanced readfish provides a powerful solution for targeted sequencing on industrial-scale nanopore platforms.
Adaptive sampling on the PromethION enables efficient and cost-effective large-scale human genome variation analysis.
This advancement facilitates deeper insights into genomic diversity and disease-associated variations.