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MinIon : The Ultimate future of genome sequencing

minion genome sequencing nanopore asic minknow metrichor

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#1 Engadin

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Posted 07 April 2019 - 12:00 AM


oxford-nanopore-minion.jpg

 

MinION device

 

Ever since the completion of the human genome project the world has started to move in a new direction. Scientist and researchers across the globe have started to investigate various types of cellular and life forms which come across the human race in our everyday life. Human genome project paved the way for entirely new form of research, instead of focusing on individual gene, waiting months or years for the results of a single gene, scientist are now focusing on a broad view research, focusing on entire genome checking for every possible gene related to certain function, analyzing combine result of all the genes, estimating importance level and impact of each gene on expression of a certain trait. For this the scientific community started to rely heavily on genome sequencing machines and tools for whole genome analysis. But with this new approach come a lot of new challenges.

 
Challenges:
Traditional sequencing machines are too large, non-portable, difficult to operate by inexperienced persons and much more. Imagine conducting a new and innovative research focused on examining biodiversity of a forest range or a mountain region or a desert or under the ocean, you come across something new an animal, an insect, or a plant which shows some physical characters and attributes which are completely new and has never been observed before question arises here is it a new form of species or a pre-existing one with slight new traits? Best way to know the answer is to analyse its genome and to cross match the results, for that you’ll have to extract DNA samples prepare genome for analysis and send it to a company in a different country or even to a different continent, the process will take weeks or months and thus increasing the overall risk for losing that new species (in case it’s a new species) or negative results may result in wasting a lot of our time. This whole laborious and lengthy procedure jeopardizes the overall productivity of such innovative research. So, was the case so far, in order to answer this problem scientist at the Oxford Nanopore Technologies inc.(an Oxford University spin-off) came up with a solution in form of MinION the world’s 1st ever portable genome sequencer.
 
MinION:
MinIOn is an innovation by the Oxford Nanopore Technologies, it is the world’s 1stever portable genome sequencer enabling real time identification and DNA analysis, the MinION enables:
     ·   Real time DNA sequencing 
     ·   Immediate availability of results
     ·   Long reads of 200kb or greater
     ·   Sequencing 10-20 GB DNA data per flow cell
     ·   450 bp per second read
     ·   Enabling research on wild samples in real time
     ·   Enabling RNA analysis without PCR
     ·   Easy installation and cost effective
     ·   No need for additional setup
     ·   Enabling multiple sample analysis
     ·   Powered via USB connection to laptops/PC
     ·  Ability to stop on purpose providing flexibility
 
HOW IT WORKS:
The key component in MinION is the nanopore; a tiny protein embedded in to a membrane layer created from synthetic polymers, the membrane is an electrically resistant one, when a current is applied through this membrane a current channel is created across the nanopore. Whenever a molecule passes through the pore it results in to a specific disruption of current which is immediately recorded and processed.
For the analysis, first of all a DNA library is created which is mixed up with a specific processing enzyme, the library is then loaded in to the MinION flow cell. Each flow cells contains a large number of nanopore, the processing enzyme attaches the DNA sample to the nanopore and passes the single stranded DNA through the pore which creates signals related to specific disruption of current. The signals are recorded and immediately processed by a special Application specific integrated circuit (ASIC). This analyses the individual strands and determine the sequence of each strand. The process feed all the data to MinKNOW computer software which controls the MinION and performs specific data analyses task, which analysis is to be conducted, what data task to be performed, length and duration of the task all is managed through the MinKNOW. The MinKNOW further uploads all the data to METRICHOR an online cloud based bioinformatics platform, this enables real time sequence analysis of DNA and provides answer to all of our questions in real time with a required level of confidence. It gives answer to what we are searching; either it is a gene mutation, a single nucleotide mutation/polymorphism(SNP), a new strain of virus or bacteria or an entirely new species all in real time.
 
MinION%2Bdata.png
 
Image showing DNA passing through nanopore and data produced in real time
 
Current Researches:
The MinION is being widely used by the scientists related to every field, currently it’s being used for:
·         For rapid on field identification of various human,animal & plant pathogen
·         For detection of life forms in high altitude permafrost of Canada
·         Analysing various marine virus strains
·         Identification of viral strains in cassava crop in Africa
·         Analysing mutations in cancerous cells
·         Exploring biodiversity in Amazon rainforest
·         On field diagnosis of plant diseases
 
Conclusion:

With the rapid evolution of human race, with a rapid transition in to the modern world come new challenges to human life. Many of the challenges faced by human are related to some type of cellular or biological form (i.e; bacteria, fungus, amoeba, etc.) and best way to resolve it is to know the genomic basis of that certain entity, once we know the genetic basis, the genes involved in growth and survival of that entity, once we have tracked them, we can develop an effective strategy to combat with it. The MinION genome sequencer is revolutionizing the way with which we perform our research, introducing an entirely new element and enabling researchers to move freely and perform experiments any where possible and under every possible environment.

 

Source: https://crisprpedia....-of-genome.html

 

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Also tagged with one or more of these keywords: minion, genome sequencing, nanopore, asic, minknow, metrichor

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