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Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....

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Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Candidate Gene Testing in Clinical Cohort Studies with Multiplexed Genotyping and Mass Spectrometry

Published on: June 21, 2018

Genotyping by multiplexed sequencing (GMS): A customizable platform for genomic selection.

Travis M Ruff^1,2, Elliott J Marston³, Jonathan D Eagle³

¹Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America.

|May 2, 2020

Summary

We developed a new PCR-based genotyping method for high-throughput analysis of thousands of single nucleotide polymorphism (SNP) markers. This genotyping by multiplexed sequencing (GMS) approach offers accurate and reliable results, validated against existing technologies.

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Infinium Assay for Large-scale SNP Genotyping Applications

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Area of Science:

Genetics
Molecular Biology
Bioinformatics

Background:

Genotyping technologies are advancing in throughput and multiplexing.
High-throughput genotyping is crucial for genetic studies and breeding programs.

Purpose of the Study:

To introduce a novel, high-throughput, PCR-based genotyping technology.
To demonstrate a user-friendly bioinformatic pipeline for interpreting genotyping data.

Main Methods:

A two-step PCR approach for multiplexing thousands of single nucleotide polymorphism (SNP) markers.
Genotyping by multiplexed sequencing (GMS) protocol tested on Triticum aestivum L. recombinant inbred line (RIL) populations.
Sequencing compatibility with Ion Torrent and Illumina next-generation sequencing (NGS) platforms.

Main Results:

The GMS protocol successfully multiplexed 1,656 wheat SNP markers, 207 barley SNP markers, and 49 informative markers, yielding up to 2,433 data points.
100% agreement was observed between GMS data and existing Illumina Infinium assay data for two RIL populations.
Direct sequencing products offer enhanced reliability compared to scatter plot analysis from other methods.

Conclusions:

The GMS method provides a reliable, high-throughput, and user-friendly solution for SNP genotyping.
This technology is adaptable to different NGS platforms, offering flexibility for researchers.
The accuracy and agreement with existing data validate GMS as a robust genotyping approach.