Next Generation Sequencing
About the Next Generation Sequencing Virtual Lab Simulation
In the Next Generation Sequencing (NGS) simulation, you will obtain a hair sample from an ancient man from Greenland, extract his DNA, and perform DNA sequencing. The NGS technology uses second-generation DNA sequencing, where users perform sequencing of many samples at the same time, also known as massive parallel sequencing. NGS has many real –life application scenarios. In this lab specifically, you will use SNP (Single Nucleotide Polymorphism) analysis to correlate the result with physical appearance such as hair baldness, earwax thickness and many others. By looking at the SNP result, you will learn how to reconstruct the physical appearance of the ancient man from Greenland.
Understanding the steps from DNA to sequencing results
In the first part of the Next Generation Sequencing lab, you will be taken through the multiple steps of sample preparation and sequencing process and learn about sample fragmentation, end repairing, A-tailing and PCR amplification of the sample. You will then proceed to the sequencing machine where you will perform cluster generation followed by the sequencing reaction and data collection. These processes will be illustrated with 3D animations as well as quiz questions.
Data processing and analysis
After completing the sequencing procedure, you will acquire the data outcome as a FASTQ file. Your next task is then to process them. Using the command lines, you will learn to perform quality control for the data, eliminate degraded and contaminated DNA, trim out the adapters, map the sequence to a reference genome, and perform the SNP analysis. By comparing the SNP profiles, you can study the pattern of migration. You can also look at specific SNPs, for example, the ones that result in amino acid change and give rise to a specific physical characteristic such as hair baldness or ear wax thickness. Please note that data processing and analysis presented in this lab can be adapted to other data analysis tools suitable for different courses.
Learn all about sequencing
The Next Generation Sequencing lab highlights sample preparation and sequencing procedures—which are constant regardless of different downstream applications. By going through the virtual lab, you will get a thorough understanding of the multistage processes of obtaining a DNA sample, and be able to use this to find the sequencing result and perform an analysis.
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Techniques In Lab
- Next generation sequencing
At the end of this simulation, you will be able to…
- Understand the different steps in sample preparation, cluster generation, sequencing and data processing
- Understand the characteristics of ancient DNA
- Understand that Single Nucleotide Polymorphism (SNP) can be tightly correlated to a specific physical feature
Screenshots of Next Generation Sequencing Virtual Lab Simulation
Dr. Simon Rasmussen
Center for Biological Sequence Analysis, Department of System Biology
Technical University of Denmark
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