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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.

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...

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Related Experiment Video

Updated: Jun 23, 2026

Infinium Assay for Large-scale SNP Genotyping Applications

Infinium Assay for Large-scale SNP Genotyping Applications

Published on: November 19, 2013

High-throughput genotyping by whole-genome resequencing.

Xuehui Huang¹, Qi Feng, Qian Qian

¹National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.

Genome Research

|May 8, 2009

Summary

A new high-throughput sequencing method enables faster and more precise genetic mapping in rice. This genome-based genotyping approach improves recombination breakpoint determination and aids in gene discovery.

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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

Area of Science:

Genomics
Molecular Biology
Plant Science

Background:

Next-generation sequencing and expanding genome databases offer opportunities to refine genetic mapping and analysis strategies.
Traditional genotyping methods can be time-consuming and less precise for determining recombination breakpoints.

Purpose of the Study:

To develop a high-throughput, genome-based method for genotyping recombinant populations using whole-genome resequencing data.
To improve the accuracy and resolution of genetic maps and facilitate quantitative trait locus (QTL) discovery.

Main Methods:

Utilized whole-genome resequencing data from Illumina Genome Analyzer for genotyping.
Developed a sliding window approach to analyze genome-wide single nucleotide polymorphisms (SNPs) for genotype calling and recombination breakpoint identification.
Constructed a genetic map for 150 rice recombinant inbred lines.

Main Results:

Achieved a genotype calling accuracy of 99.94% and recombination breakpoint resolution within an average of 40 kb.
The sequencing-based method was approximately 20x faster and 35x more precise than PCR-based marker methods.
Successfully located a large-effect quantitative trait locus for plant height in a 100-kb region near a key rice gene.

Conclusions:

The developed genome-based genotyping method is robust, feasible for various organisms, and offers significant advantages over conventional marker-based approaches.
This method provides a powerful tool for large-scale gene discovery and addressing complex biological questions in genomics.
The approach is adaptable to different mapping populations, genome qualities, sizes, and polymorphism levels.