Next Generation Sequencing 1: Overview - Eric Chow (UCSF)

Introduction

This tutorial provides an overview of next generation sequencing (NGS), a revolutionary technology that allows for rapid and cost-effective DNA sequencing. You will learn the basics of how NGS works, tips for preparing and running samples, and insights into its applications in medical diagnostics.

Step 1: Understanding the Basics of Next Generation Sequencing

Next generation sequencing differs significantly from traditional methods like Sanger sequencing. Here are the key points:

• Efficiency: NGS can sequence a human genome in about 48 hours for around $1,000, compared to the 20 years and $3 billion required for the Human Genome Project using Sanger sequencing.
• Technology: NGS platforms, such as those from Illumina, use imaging techniques to detect the addition of fluorescently labeled nucleotides during the sequencing process.

Step 2: Sample Preparation

Proper sample preparation is crucial for successful sequencing. Here are some practical steps:

1. Purifying DNA Samples:

   • Use magnetic beads for effective purification.
   • Ensure that the DNA is free from contaminants that could interfere with sequencing.

2. Assessing Sample Quality:

   • Utilize an Agilent Bioanalyzer to check the quality of your nucleic acid samples.
   • Look for appropriate size distribution and concentration to ensure optimal sequencing results.

Step 3: Sequencing Technologies

Different NGS technologies offer various benefits and drawbacks. Familiarize yourself with these options:

• Illumina Sequencing:

  • Advantage: High throughput and low error rates.
  • Disadvantage: Shorter reads compared to some other technologies.

• Alternative Technologies:

  • Some methods allow for longer reads, which can be beneficial for specific applications.
  • Keep in mind that longer reads may come with higher error rates.

Step 4: Medical Applications of NGS

Next generation sequencing has significant implications in the medical field:

• Prenatal Testing:

  • NGS allows for less invasive testing methods to assess fetal health.

• Cancer Detection:

  • It enables the identification of mutations associated with various cancers, leading to better diagnosis and treatment strategies.

Conclusion

Next generation sequencing is a powerful tool that has transformed the field of genomics. By understanding the basics, preparing samples correctly, and being aware of the different technologies and their applications, you can effectively utilize NGS in your research or clinical practice. Consider exploring further resources or seeking hands-on experience to deepen your understanding of this innovative technology.