The field of genomics has been growing at an exponential scale ever since the invention of the sequencing technique. In contrast to the first-generation method like Sanger’s chain termination sequencing which took over a decade to sequence the entire human genome, NGS is a second-generation method that holds the potential to do the same task in a day. That’s the power of Next generation sequencing!
NGS, being an advanced sequencing technology, is proving its potential in varied fields like medical diagnostics, agricultural biotechnology, novel gene discovery and genetic therapeutics. It uses multiple short DNA molecules that are sequenced in parallel; thereby being called the “massively parallel sequencing” too. Since multiple short sequences are decoded in tandem, it not only saves a lot of time and effort but also makes the data for downstream applications more reliable and scalable. Without any doubt, we can proclaim NGS as a revolutionary technology of modern science.
When this technique possesses such a charm and potential to solve the modern-day complex genomics questions, why does NGS intimidate a large bunch of students?
Why do students seem hesitant to participate in discussions regarding this technology, its procedures, associated analytical tools, and its practical applications?
In this article, we’ll shed light on all these issues. Even though NGS has successfully filled the gap between ‘demands of the practical world’ and ‘the capabilities of 1st generation sequencing’, the gap between NGS and students persists.
Educators dealing with NGS courses often face the same bridging this gap. This article can provide some help to educators as it highlights the major issues encountered by students. It also lists practical solutions to resolve them. By the end, we’ll share why a virtual lab simulation will prove useful not only for your students but also for you as an educator to deliver concepts more efficiently.
There are 3 reasons why students dread and get confused about the topic of NGS. Acknowledging these blocks is the first step toward making the topic more approachable.
Unlike the easier protocol of Sanger’s sequencing or any other 1st generation sequencing technique, the NGS protocol is quite complicated. Students are intimidated by the complex processes of sample preparation where a range of criteria need to be ensured. DNA samples need to be modified by the addition of adaptors. Nucleotides should be modified by the addition of fluorophore and a 3’ cap. Only a certain DNA polymerase (T4 pol) can be used for nucleotide addition. Only a machine with a sequencing chip that has a flow cell can be utilized. On top of all this, introduction to the novel concept of sample fragmentation, cluster generation, end repairing, and A-tailing of the sample often leaves students in despair.
The generation of great depth of information using the NGS technology is of no use if one isn’t capable of rationally sorting, cleaning, processing and analyzing data. Since the raw data is very heavy, sometimes processing the data files becomes a problem for students on traditional computer systems available on school and college campuses. The analysis in itself is also complex comprising 3 subtypes; primary, secondary and tertiary analyses. Lack of knowledge about output data files and their different formats (fasta, fastq, etc), data filtering and Phred quality scores, adaptors trimming using bioinformatics tools, different types of read assembly (de novo, comparative), and many such topics amongst students makes the work tremendously hard for educators as it is for students.
Students don't frequently work with NGS equipment because of the high expenses of the equipment and the consumables needed to perform NGS. Being less acquainted with the technology, they aren’t able to explore its full potential. Moreover, it can be challenging to find successful research examples where NGS’s contribution was instrumental. This lack of information makes students undervalue this gem technology which if used to its full potential can help research reach pinnacles of success.
To address the blocks encountered while teaching NGS, educators can engage the under-listed solutions in their classes. These can clarify many instrumental aspects of NGS. Not only can they make teaching easier for educators like you but they will also make lessons clearer and easier to assimilate for your students.
This advice can come in handy when your students are practicing performing the experiments in their lab sessions. Why, how and when are some important questions that every science researcher must always ask. Adding any chemical to the reaction or PCR or sequencing mixture without knowing its specific role and necessity in the experiment is not real science.
So, boost your students to ask why they are performing every single step of NGS. This will hone their art of setting reactions without wasting chemicals and their most precious thing; time. You can begin with some very basic topics and portray some reasoning-based questions for students to find answers to; a few of them are listed below:
What is the need for fluorophores on the nucleotides? (Ans: detection)
Why is a 3’ cap attached to all the nucleotides? (Ans: to ensure that only 1 nucleotide is added at a time i.e. to block elongation)
How is the blocking site at the 3’ terminal removed to incorporate the next incoming nucleotide? (Ans: chemical removal)
Why are adaptors added to the sample DNA? (Ans: for the binding to the NGS flow cell)
Such reasoning-based questions will compel your students to think critically when they add each chemical or set a reaction condition. They won’t have to cram the details, instead, they can synthesize their reaction mixtures.
Many students are oblivious to basic biotechnology and molecular biology concepts. Before teaching them the extensive bioinformatics and computational biology concepts for NGS data analysis, their core concepts must be firmly established. Many concepts may seem elementary to educators, but for students, they can occasionally be very challenging. We list a few of them that generally hassle the major bunch of students.
Use of Adaptors for DNA amplifications and Sequencing
Sticky ends versus Blunt ends
Different types of DNA polymerases and their various activities (proofreading activity, terminal transferase activity)
DNA complementarity and its use in the adenylation process (poly-A tails)
PCR amplification with adaptor-specific primers (You can use the PCR simulation from Labster for explaining more about the topic)
SNPs and how they manifest
Relation of genotypic changes to phenotypic traits
Figure: Adenylation (addition of Poly-A tails) of the sample DNA helps in the ligation process between sample DNA and adaptors with poly-T tails. This exploits the basic law of DNA complementarity (A bonds with T with a double bond). Image Source
You can add more fundamental topics to your list and try to conduct engaging discussions in your next class. You’ll be able to see the results when your students practically handle the NGS after this small activity.
Since the NGS topic is undoubtedly rich in information and peculiarities of each step, using infographics that can deliver the crux of the information can work as guiding posts for your students as they practically set up experiments in the lab. As observed, it’s difficult for students to read through the lines of textbooks and traditional lab protocols. Making them colorful and interactive could be a wonderful way to leave students with more knowledge and information.
Figure: A flowchart showing the steps of the NGS experiment. Image Source
Even for the NGS data analysis, using informative illustrations and figures can ease the work of the students to understand bioinformatics concepts like the Phred score, output data files, etc.
Figure: An infographic showing details about the output data files and criteria used for data filtering in the NGS technique. Image source
Also, many research labs don’t have sufficient funds to ensure the practical handling of NGS instrumentation. Some don’t even have funds for 1 single demonstration by the educators. This scenario can deprive students of the chance to explore NGS technology. In such cases, educators can try to source visually interactive videos and simulations that can serve as virtual alternatives for lab handling sessions. Labster’s NGS simulation can also be used as it provides several options to conduct a fun-filled learning session for students.
Students are often unaware of the many practical applications of NGS technology. Without enough information about its’ real-world utility, learning the technique and its complex analysis (which no doubt requires one to learn a lot of bioinformatics and computational biology tools) can be very tiresome and taxing. We list some of the uses of NGS that you can explain to our students.
For whole genome sequencing
For RNA sequencing (RNA-Seq) and discovering novel RNA variants (You can useBioinformatics simulation for explaining how NGS is used in RNA-Seq)
For exploring genetic reasons for cancers and tumors (in oncology)
For studying new infectious agents (like SARS-CoV-2 virus genome and variants) (in microbiology)
For genetic testing and gene therapies
For understanding the characteristics of ancient DNA (You can use the NGS simulation by Labster where your students can enter a virtual laboratory that allows them to obtain a hair sample from an ancient man from Greenland, extract his DNA, and perform DNA sequencing. They will use SNP analysis for correlating the result with physical appearances such as hair baldness, earwax thickness and many others).
Figure: This snippet from the NGS simulation by Labster helps your students in engaging in a virtual experiment where they collect ancient DNA and sequence it using NGS technology. It is available for University / College and Professional classes.
Since NGS is a very wide topic to teach to young learners with only conventional tools at hand, educators often feel troubled delivering their points in class. With a lack of practical handling opportunities, it can also become quite a passive topic to teach.
With virtual laboratory simulations from Labster, teachers can make more insightful points as students are rendered with better visual options. The 3-D simulations help them better understand how the steps of each analysis advance and results are delivered.
Your students don’t have to struggle to imagine different aspects of this topic themselves as our interactive NGS simulation along with gamification elements come to the rescue. The different processes of NGS are illustrated with 3D animations as well as quiz questions.
By using this way of active and immersive teaching, our virtual learning platform takes an advent in the field of Science to make the upcoming scientists thorough with the “basics of their respective subjects”.
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