Next Generation Sequencing Virtual Lab
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About the Next Generation Sequencing Virtual Simulation Lab
In the NGS Simulation students obtain a hair sample from an ancient Greenland man, 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. Specifically, this lab 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, students can reconstruct the physical appearance of the ancient Greenland man.
Understanding the steps from DNA to sequencing results
Students are taken through the multiple steps of sample preparation and sequencing process learning about sample fragmentation, end repairing, A-tailing and PCR amplification of the sample. Students will then proceed to the sequencing machine where they will perform cluster generation followed by the sequencing reaction and data collection. These processes will be illustrated using 3D animations supplemented with quiz questions.
Data processing and analysis
After completing sequencing procedure, students will acquire the data outcome as a FASTQ file and process them. Using the command lines, students will 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, students study the pattern of migration. Students will also look at specific SNPs, especially the ones that result in amino acid change and give rise to a specific physical characteristic, such hair hair baldness or ear wax thickness.
Data processing and analysis presented in this lab can be adapted to other data analysis tools that are suitable for your course.
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, students will understand the multistage processes of obtaining a DNA sample to getting the sequencing result and perform analysis.
Dr. Simon Rasmussen
Center for Biological Sequence Analysis, Department of System Biology
Technical University of Denmark
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