Build the Read: A Hands-On Activity for Introducing Microbiology Students to Next-Generation DNA Sequencing and Bioinformatics †
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Authors:
Guerrino Macori1,*,
Angelo Romano2,
Lucia Decastelli2,
Paul D. Cotter1
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Received 04 June 2017 Accepted 08 August 2017 Published 01 December 2017
- ©2017 Author(s). Published by the American Society for Microbiology
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[open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.
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†Supplemental materials available at http://asmscience.org/jmbe
- *Corresponding author. Mailing address: Teagasc Food Research Centre, FoodBiosciences Department, Moorepark, Cork, Ireland. Phone: +353 (01) 805 9531. E-mail: [email protected].
Abstract:
Next-Generation Sequencing (NGS) is the current standard for providing genomic data, by virtue of the ability of the technology to generate a considerable amount of information rapidly and at low cost. The data generated can be of key importance to research and addressing issues in public health and, thus, is relevant to society. Unsurprisingly, content relating to the principle and chemistry underlying Next-Generation Sequencing is presented to almost every microbiology-related class, to professionals across multiple fields and, to the general public as popular science. The most commonly utilized NGS platforms (MiSeq, NextSeq and HighSeq) are those provided by Illumina. In this paper, we describe a hands-on activity for students to represent the chemistry underlying Illumina-based NGS, by creating representative reads using LEGO blocks, to link indexes, assemble the sequence and ‘identify’ the bacteria from which the DNA originated, thereby, in the process introducing the participants to the basic principles of bioinformatics.
References & Citations
Supplemental Material
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Appendix 1: Lecture copy, Appendix 2: List of materials and instructor’s notes, Appendix 2: Exercise forms 2a/2b/2c/2d/2e/2f, Appendix 3: Reference genomes table, Appendix 4: Tables for recording the sequences obtained, Appendix 5: Formative assessment quiz, Appendix 6: Results of the pre- and post-quiz (pilot activity)
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Abstract:
Next-Generation Sequencing (NGS) is the current standard for providing genomic data, by virtue of the ability of the technology to generate a considerable amount of information rapidly and at low cost. The data generated can be of key importance to research and addressing issues in public health and, thus, is relevant to society. Unsurprisingly, content relating to the principle and chemistry underlying Next-Generation Sequencing is presented to almost every microbiology-related class, to professionals across multiple fields and, to the general public as popular science. The most commonly utilized NGS platforms (MiSeq, NextSeq and HighSeq) are those provided by Illumina. In this paper, we describe a hands-on activity for students to represent the chemistry underlying Illumina-based NGS, by creating representative reads using LEGO blocks, to link indexes, assemble the sequence and ‘identify’ the bacteria from which the DNA originated, thereby, in the process introducing the participants to the basic principles of bioinformatics.

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Author and Article Information
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Received 04 June 2017 Accepted 08 August 2017 Published 01 December 2017
- ©2017 Author(s). Published by the American Society for Microbiology
-
[open-access] This is an Open Access article distributed under the terms of the Creative Commons Attribution-Noncommercial-NoDerivatives 4.0 International license (https://creativecommons.org/licenses/by-nc-nd/4.0/ and https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode), which grants the public the nonexclusive right to copy, distribute, or display the published work.
-
†Supplemental materials available at http://asmscience.org/jmbe
- *Corresponding author. Mailing address: Teagasc Food Research Centre, FoodBiosciences Department, Moorepark, Cork, Ireland. Phone: +353 (01) 805 9531. E-mail: [email protected].
Figures
Bricks fixed in the flow-cell. In the simulation are represented 8 reads of 7 bases, each with indexes of 3 base lengths. (See Appendix 2 for the list of materials and notes for the instructor.)

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FIGURE 1
Bricks fixed in the flow-cell. In the simulation are represented 8 reads of 7 bases, each with indexes of 3 base lengths. (See Appendix 2 for the list of materials and notes for the instructor.)
Simulation of part 1 and part 2 of the exercise The picture shows the reads that have been built with their indexes (a) and their overlapping (b), assembling a contig.

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FIGURE 2
Simulation of part 1 and part 2 of the exercise The picture shows the reads that have been built with their indexes (a) and their overlapping (b), assembling a contig.
Possible extensions of the exercise. Simulation of the amplification and cluster generation. The hand simulates the consequential addition of bases during the sequence by synthesis reaction while the smartphone acquires the sequential pictures, simulating the solid-phase cluster amplification and acquisition of the images of the flow-cell by sequencers.

Click to view
FIGURE 3
Possible extensions of the exercise. Simulation of the amplification and cluster generation. The hand simulates the consequential addition of bases during the sequence by synthesis reaction while the smartphone acquires the sequential pictures, simulating the solid-phase cluster amplification and acquisition of the images of the flow-cell by sequencers.