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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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Related Experiment Video

Updated: Mar 27, 2026

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

Quantifying Next Generation Sequencing Sample Pre-Processing Bias in HIV-1 Complete Genome Sequencing.

Bram Vrancken¹, Nídia Sequeira Trovão², Guy Baele³

¹Rega Institute for Medical Research, Clinical and Epidemiological Virology, Department of Microbiology and Immunology, KU Leuven-University of Leuven, 3000 Leuven, Belgium. bram.vrancken@rega.kuleuven.be.

|January 12, 2016

Summary

This summary is machine-generated.

Near full-genome sequencing of HIV is crucial for understanding drug resistance and viral evolution. This study compares fragmentation methods for next-generation sequencing (NGS), finding minimal impact from fragmentation type on results.

Keywords:

HIV NGS full genome sequencing

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Last Updated: Mar 27, 2026

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Published on: January 30, 2019

Area of Science:

Virology
Genomics
Molecular Biology

Background:

Genetic analyses are vital in infectious disease research, particularly for HIV.
Current methods often focus on small genomic regions, limiting comprehensive analysis.
Next-generation sequencing (NGS) for RNA viruses is hindered by high input DNA requirements.

Purpose of the Study:

To develop and evaluate a near full-genome amplification protocol for HIV.
To compare enzymatic fragmentation (Nextera™) with mechanical shearing for Roche 454 sequencing.
To assess the impact of fragmentation methods on characterizing viral population composition.

Main Methods:

Utilized a generic overlapping amplicon-based protocol for near full-genome amplification.
Compared low-input enzymatic fragmentation (Nextera™) against conventional mechanical shearing.
Applied the protocol to deep sequence pre-therapy plasma and peripheral blood mononuclear cell (PBMC) samples.

Main Results:

Fragmentation method had a modest impact on characterizing viral population composition.
Variations across all procedural steps (nucleic acid extraction to sequencing) are critical for reliable results.
Near complete genome sequencing offers significant benefits for routine HIV genotyping.

Conclusions:

The chosen fragmentation method has limited influence on HIV population composition analysis.
Controlling variability throughout the entire NGS workflow is essential for accurate results.
Near full-genome sequencing is a valuable approach for clinical applications like drug resistance testing.