MinION as a Teaching tool in a Graduate course in Pakistan

Wahid Ullah, Ikram Ullah, Gohar Rahman, Nasir Khan, Khawar Sohail, Muhammad Ilyas

Abstract


Genomics is a rapidly evolving field of study that is increasingly being utilized as a tool to detect ethnic and tribal-specific mutations that may be the key to rare and common diseases with higher prevalence in the population under study [1]. However, researchers and science educators in remote areas can often find it difficult to access the latest genetic technologies, probably due to its high costs and lack of suitable infrastructure. Recent technological innovations are resulting in portable, low-cost instruments that enable next-generation sequencing in remote environments, offering new opportunities to generate a more widespread network of trained geneticists [2]. We need to formalize educational efforts to teach students and young researchers with hands-on training to excel in molecular and bioinformatics knowledge. Here, we report our experience of using the MinION pocket size sequencer in a graduate course. The graduate course had some theoretical lectures that explained the basic principles of genomics followed be practical sessions. We hope that the training material developed during this course will provide the community with useful tools to help educate future generations of genome scientists in Pakistan. 


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References


Sivasubbu S, Scaria V. Genomics of rare genetic diseases—experiences from India. Human genomics, 2019; (1): 1-8.

Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nature Reviews Genetics, (2016); (6): 333.

Laver T, Harrison J, O’neill PA, Moore K, Farbos A, Paszkiewicz K, Studholme DJ. Assessing the performance of the oxford nanopore technologies minion. Biomolecular detection and quantification, (2015); 1(3): 1-8.

Franus W, Kuśmirek W, Nowak RM. Scaffolding algorithm using second-and third-generation reads. InPhotonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments (2018); (Vol. 10808, p. 108083A). International Society for Optics and Photonics.

Wang J, Moore NE, Deng YM, Eccles DA, Hall RJ. MinION nanopore sequencing of an influenza genome. Frontiers in microbiology, (2015); 18(6): 766.

Mikheyev AS, Tin MM. A first look at the Oxford Nanopore MinION sequencer. Molecular ecology resources, (2014); 14(6): 1097-102.

Imai K, Tarumoto N, Misawa K, Runtuwene LR, Sakai J, Hayashida K, Eshita Y, Maeda R, Tuda J, Murakami T, Maesaki S. A novel diagnostic method for malaria using loop-mediated isothermal amplification (LAMP) and MinION™ nanopore sequencer. BMC infectious diseases, (2017); 17(1): 621.

Nica I, Wotawa F. Diagnosis-based reconfiguration using the MINION constraint solver. InProceedings of the 22nd International Workshop on Principles of Diagnosis (DX 2011) (2011); 225-232.

Ilyas M, Sadique S, Masood K, Qamar R, Chohan SN. The development of computational biology in Pakistan: still a long way to go. PLoS computational biology, (2011); 7(6): e1001135.

Stubbs S, Blacklaws B, Yohan B, Yudhaputri FA, Schwem B, Salvana EM, Destura RV, Myint KS, Sasmono RT, Frost SD. A Nanopore-based method for generating complete coding region sequences of dengue virus in resource-limited settings. bioRxiv. (2018); 499111.

Lu H, Giordano F, Ning Z. Oxford Nanopore MinION sequencing and genome assembly. Genomics, proteomics & bioinformatics, (2016); 14(5): 265-79.

Cao MD, Ganesamoorthy D, Cooper MA, Coin LJ. Realtime analysis and visualization of MinION sequencing data with npReader. Bioinformatics, (2015); 32(5): 764-6.

Langmead B. Aligning short sequencing reads with Bowtie. Current protocols in bioinformatics, (2010); 32(1): 11-7.

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics, (2009); 25(16): 2078-9.




DOI: http://dx.doi.org/10.62940/als.v7i4.933

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