MinION as a Teaching tool in a Graduate course in Pakistan

MinION as a Teaching tool in a Graduate course in Pakistan

Abstract

Gnomics 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 nextgeneration 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.
MinION is probably the first commercially available sequencer which uses nanopore technology [3]. It is a small
100gm palm size USB interfaced portable sequencer and can be connected to the computer through USB 3.0 port
[4]. As every researcher, from under developing countries like Pakistan cannot afford their very own sequencer
(Illumina, Ion torrent or Sanger sequencer etc.) for the research purposes. As the currently available sequencers are
not only expensive in cost at the time of purchase but also need a high value maintenance which is also provided by
the concerned companies at quietly affective cost. This make nearly impossible to use the advanced expensive
technology of sequencing by the researchers at newly developed research facilities. Still there are about seven
different institutions in Pakistan that have installed next generation sequencers like Illumina HiSeq, MiSeq, Ion
Torrent, 454 etc. Most of them are not functional for the last many years. Keeping insight all these challenges faced
by researchers Oxford Nanopore Technologies designed this very new technology MinION and its variant GridION,
PromithION and SmidgION all of them uses the same technology and same platform except SmidgION which can be
used with a smart phone at any remote location [5]. Considering the requirement of its low budget and need of no
extra gadget as compared to other present technologies which requires high budget and plenty of other equipment
MinION will be the future of DNA sequencing [6]. As it has lower cost, easily portable, easy to use and quite precise
in performance, this technology has a bright future in developing countries and also in disaster hit areas for diagnostic
purpose [7]. This will allow us to investigate different medical cases on the spot [8].
The Centre for Omic Sciences at Islamia College University Peshawar was established in early 2017 with a mission
to bring Pakistan on the map of genomics and computational biology (http://genomelab.icp.edu.pk). This centre is on
the hunt for the best brains amongst the young scholars to prepare the next generation scientists, innovators and bioentrepreneurs. The team is striving for developing computational biology in Pakistan since 2011 [9]. The genomics
course was proposed in the MPhil and PhD curriculum in 2018 and was approved by the Academic council of the
university. It was offered in spring 2019 to the graduate students. State of the art topics have been added in the
course including practical sessions on MinION nanopore. Since we can not afford the big sequencers machine neither
we have funds to run it, therefore this pocket size sequencer is much better for the students to understand the basics
of sequencing.
The course started with the introduction of genomics and computational biology. Students were taught about basics
of bioinformatics including databases, alignment tools, primer designing, phylogenetics, protein modelling and
docking etc.

 

No. of Pages
190-192
Volume
7
Author's Details
Wahid Ullah, Ikram Ullah, Gohar Rahman, Nasir Ali, Khawar Sohail, Muhammad Ilyas
Research Field
Bioinformatics