Bi426 Tutorial 7 (1)

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Jan 9, 2024

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Tutorial 7 Kennydi Farquharson, 190285230 Shakiraa Suntharalingam 200823270 Wilfrid Laurier University has decided to invest in a second-generation sequencer and needs your help deciding which technology to invest in. Your research group has been contracted to help WLU determine which next-generation sequencer best fits the school's needs and budget. The school is looking for a cost-effective way to quickly sequence DNA. Your job is to review the available literature for each technology, compare and contrast the technologies, and determine which method you think the school should adopt. Consider factors such as the technology's accuracy, read length, time to run, and cost. It is up to you to decide which factors you consider most important, but make sure to provide a strong rationale for your ultimate choice. The technologies you may research include the following: ● Illumina ● 454 ● SOLiD ● Pacific Bio ● Ion Torrent Sequencing ● Any newer, better technologies? In order to complete your goal, do the following: 1. Select which technology you think is best. Justify your reasons based on your research. Discuss the criteria you considered the most important. How does this technology compare/contrast with the others? What are the strengths and the weaknesses relevant to your technology? (1-3 paragraphs) After researching each of the listed sequencing technologies, I realized that there are better technologies, this being the Sanger sequencing. Sanger sequencing is a better option for sequencing a low number of targets (1-20) compared to others as some strengths it takes is being cost effective for a single sample, and not relying much on computational tools compared to others. Sanger is able to be very specific when it comes to testing the variants when all being a part of the same family. It also doesn't require extensive validation as the Sanger sequencing method is verified on a single/small number of sequences (Shrestha, 2023). Why Sanger sequencing stands out compared to the rest is because they are able to identify microbes, analyze fragments and short-tandem repeats (STR’s), (Shaffer 2019). While Sanger sequencing is the best option it also has its shares of weakness.It sequences short fragments of DNA about 300-1 kb bases while requiring more DNA input, and consumes a lot of time. It cannot detect different genes simultaneously as Sanger does have low sensitivity which results in the limit of detection, while using it with a low discovery power. Lastly it is also not as

cost effective when it comes to using a high number of targets, about 20 or more (Shrestha 2023). The most important aspect to choosing the best sequencing technology in my opinion is accuracy. Of course, considering the read length, time to run and cost was also used in this decision as well. If an institution is purchasing such an expensive machinery in the first place they have the money to afford the best and most accurate reading. This would help to further research while ensuring there are little mistakes. The accuracy of Sanger sequencing is incredibly high at 99.99%, the error rate less than 0.001%. The errors are mainly due to the DNA sample being of poor quality, or the primers are not the correct length (McGrath, 2014). When comparing Sanger to other technologies from the list, there are advantages and disadvantages for each process. Illumina is able to sequence short reads and it is less expensive however, it has more technical issues and a lower accuracy compared to sanger (Meszaros, 2023). The 454 sequencing has longer reads however once again the accuracy we are looking for is not there. Looking at SOLid the accuracy is 99% but still not on the same level when compared to Sanger sequencing. Pacific bio is a good contender as it can handle long reads, giving more information than technologies that only give short reads, however this is a very costly process (Meszaros, 2023). Once again it is fairly accurate but has a greater error rate than Sanger. The ion torrent is able to read lengths of various sizes, but its accuracy is 97%. 2. At the end of your discussion, include an annotated bibliography with at least 3 academic sources. This should include a consistent citation format, a brief summary of the paper, and a statement on why the citation is relevant. These are the references used during research to help us determine the best sequencing technology for the school. Each of these citations are relevant to the paper as the topics include Sanger sequencing or many of the other sequencing technologies that are listed above. After researching and comparing the technologies, illumina, 454, SOLid, pacific bio and ion torrent we found that there is a better technology being Sanger sequencing.

References: McGrath K. (2014, December 11). Sanger Sequencing Troubleshooting Guide . AGRF. Vol 1.1. Meszaros E. (2023, August 3). Sanger Sequencing vs NGS. INTEGRA. Shaffer, Dr. C. (2019, February 26). Sanger sequencing and next-generation sequencing compared . News. Shrestha, A. (2023, October 18). Sanger sequencing method: Principle and steps • microbe online . Microbe Online.

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