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Related Experiment Video

Updated: May 10, 2025

Sequencing of mRNA from Whole Blood using Nanopore Sequencing
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Barcode-free multiplex plasmid sequencing using Bayesian analysis and nanopore sequencing.

Masaaki Uematsu1, Jeremy M Baskin1,2

  • 1Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, United States.

Elife
|April 25, 2025
PubMed
Summary
This summary is machine-generated.

We developed a computational method, SAVEMONEY, to multiplex plasmids for nanopore sequencing. This approach significantly reduces the cost of whole-plasmid sequencing, making it more accessible for life science research.

Keywords:
Bayesian analysiscomputational biologyhumannanopore sequencingplasmid sequencingsystems biologywhole-plasmid sequencing

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Plasmid construction is fundamental in life science research.
  • Sequence verification is a major cost driver in plasmid construction.
  • Long-read sequencing offers whole-plasmid analysis but remains costly for routine use.

Purpose of the Study:

  • To develop a cost-effective method for routine whole-plasmid sequencing.
  • To enable multiplexing of multiple plasmids for nanopore sequencing.
  • To reduce the cost of plasmid sequence verification.

Main Methods:

  • Developed SAVEMONEY (Simple Algorithm for Very Efficient Multiplexing of Oxford Nanopore Experiments for You), a computational approach.
  • Implemented pre-survey steps for optimal plasmid mixture design.
  • Utilized post-analysis including sequence classification, alignment, and Bayesian consensus determination.

Main Results:

  • SAVEMONEY allows mixing and computational de-mixing of multiple plasmids.
  • Plasmids differing by as few as two bases can be multiplexed.
  • Accurate consensus sequencing was maintained for up to six plasmids per 180 reads.

Conclusions:

  • SAVEMONEY democratizes whole-plasmid sequencing using nanopore technology.
  • The method significantly lowers the effective cost of whole-plasmid sequencing.
  • This approach makes nanopore sequencing more competitive with Sanger sequencing for plasmid verification.